diff --git a/MONSDA/Versions.py b/MONSDA/Versions.py
index 47d5b3dc..599d5ddd 100644
--- a/MONSDA/Versions.py
+++ b/MONSDA/Versions.py
@@ -359,6 +359,25 @@ def write_versions(config, steps, envdir, monsda_version, configfile=None, path=
 
     rows = collect_versions(config, steps, envdir)
 
+    body = ""
+    if configfile:
+        body += "# config: {c}\n".format(c=str(configfile))
+    body += (
+        "# versions as pinned in the conda env yamls of the configured tools, not queried from the running binaries\n"
+    )
+    body += "#tool\tversion\tmultiqc_module\tsteps\n"
+    for row in rows:
+        body += "\t".join(row) + "\n"
+
+    if os.path.isfile(path):
+        with open(path, "r") as existing:
+            old_body = "".join(
+                line for line in existing if not line.startswith("# MONSDA ")
+            )
+        if old_body == body:
+            log.info(logid + "Tool versions unchanged, keeping " + str(path))
+            return path
+
     with open(path, "w") as out:
         out.write(
             "# MONSDA {v}\t{ts}\n".format(
@@ -366,14 +385,7 @@ def write_versions(config, steps, envdir, monsda_version, configfile=None, path=
                 ts=datetime.datetime.now().strftime("%Y%m%d_%H_%M_%S"),
             )
         )
-        if configfile:
-            out.write("# config: {c}\n".format(c=str(configfile)))
-        out.write(
-            "# versions as pinned in the conda env yamls of the configured tools, not queried from the running binaries\n"
-        )
-        out.write("#tool\tversion\tmultiqc_module\tsteps\n")
-        for row in rows:
-            out.write("\t".join(row) + "\n")
+        out.write(body)
 
     log.info(logid + "Tool versions written to " + str(path))
     return path
diff --git a/MONSDA/Workflows.py b/MONSDA/Workflows.py
index 7d686347..1eef410b 100755
--- a/MONSDA/Workflows.py
+++ b/MONSDA/Workflows.py
@@ -2356,6 +2356,13 @@ def nf_fetch_params(
     retconf["REFDIR"] = REFDIR
     retconf["IP"] = IP
 
+    # Resolve all annotation paths to absolute paths once, so every nf
+    # process can read them reliably regardless of its own work directory
+    # (mirrors the equivalent hardening in workflows/header.smk).
+    for key in list(retconf.keys()):
+        if key.endswith("ANNO") and isinstance(retconf[key], str) and retconf[key]:
+            retconf[key] = os.path.abspath(retconf[key])
+
     return retconf
 
 
diff --git a/tests/golden/config_DTU/nf/allconditions_fastqc-trimgalore-picard-star_DTU_dexseq_subflow.nf b/tests/golden/config_DTU/nf/allconditions_fastqc-trimgalore-picard-star_DTU_dexseq_subflow.nf
index 240b5324..74b21753 100644
--- a/tests/golden/config_DTU/nf/allconditions_fastqc-trimgalore-picard-star_DTU_dexseq_subflow.nf
+++ b/tests/golden/config_DTU/nf/allconditions_fastqc-trimgalore-picard-star_DTU_dexseq_subflow.nf
@@ -152,6 +152,25 @@ process salmon_quant{
         """
     }
 }
+process decompress_annotation_dtu{
+    conda "<REPO>/envs/${params.gCOUNTENV}"+".yaml"
+    container "oras://ghcr.io/jfallmann/monsda:"+"${params.gCOUNTENV}"+"-VERSION"
+    cpus 1
+	cache 'lenient'
+    publishDir "${workflow.workDir}/../" , mode: 'link',
+    saveAs: {filename ->
+        if (filename.indexOf("log") > 0)        "LOGS/${params.gSCOMBO}/DTU/"+"${params.gCOUNTENV}"+"/decompress_annotation.log"
+    }
+    input:
+    path anno
+    output:
+    path "annotation.gtf", emit: anno_plain
+    path "log", emit: log
+    script:
+    """
+    zcat -f $anno > annotation.gtf 2> log; if [ ! -s annotation.gtf ]; then echo "ERROR: decompressed annotation from $anno is empty, check source file and filesystem" >> log; exit 1; fi
+    """
+}
 process oarfish_dtu_quant{
     conda "<REPO>/envs/${params.gCOUNTENV}"+".yaml"
     container "oras://ghcr.io/jfallmann/monsda:"+"${params.gCOUNTENV}"+"-VERSION"
@@ -163,18 +182,20 @@ process oarfish_dtu_quant{
         else                                    "DTU/${params.gSCOMBO}/"+"${params.gCOUNTENV}"+"/${params.gCONDITION}/${file(filename).getName()}"
     }
     input:
-    path bam
+    path fls
     output:
     path "*.gz", includeInputs:false, emit: counts
     path "*.log", emit: logs
     script:
+    anno = fls[0]
+    bam = fls[1]
     fn = file(bam).getSimpleName().replaceAll(/\Q_mapped_sorted\E/,"")
     lf = "${params.gCOUNTENV}_"+fn+".log"
     prefix = fn+"/"+params.gCOUNTENV
     oz = fn+"/quant.sf.gz"
     ol = fn+"_counts.gz"
     """
-    mkdir -p $fn; samtools collate -@ ${task.cpus} -o namecollated.bam $bam &>> $lf; zcat -f ${params.gDTUANNO} > $fn/annotation.gtf 2>> $lf; ${params.gCOUNTBIN} --threads ${task.cpus} --genome-alignments namecollated.bam --annotation $fn/annotation.gtf --genome-fasta ${params.gDTUREF} ${params.gCOUNTPARAMS} --output $prefix &>> $lf && rm -f namecollated.bam $fn/annotation.gtf && python3 ${params.gBINS}/Analysis/oarfish_to_salmon.py -i ${prefix}.quant -o $oz &>> $lf && ln -fs $oz $ol
+    mkdir -p $fn; : > $lf; if [ ! -s $anno ]; then echo "ERROR: decompressed annotation $anno is empty, check source file and filesystem" >> $lf; exit 1; fi; samtools collate -@ ${task.cpus} -o namecollated.bam $bam &>> $lf; ${params.gCOUNTBIN} --threads ${task.cpus} --genome-alignments namecollated.bam --annotation $anno --genome-fasta ${params.gDTUREF} ${params.gCOUNTPARAMS} --output $prefix &>> $lf && rm -f namecollated.bam && python3 ${params.gBINS}/Analysis/oarfish_to_salmon.py -i ${prefix}.quant -o $oz &>> $lf && ln -fs $oz $ol
     """
 }
 process create_summary_snippet{
@@ -345,7 +366,9 @@ workflow DTU{
                 element -> return "${workflow.workDir}/../MAPPED/${params.gCOMBO}/"+element+"_mapped_sorted.bam"
             }
         mapsamples_ch = Channel.fromPath(MAPPEDSAMPLES.sort())
-        oarfish_dtu_quant(mapsamples_ch.collate(1))
+        decompress_annotation_dtu(annofile)
+        annogtf_dtu = decompress_annotation_dtu.out.anno_plain
+        oarfish_dtu_quant(annogtf_dtu.combine(mapsamples_ch.collate(1)))
         quantcounts = oarfish_dtu_quant.out.counts
     }
     prepare_dtu_annotation()
diff --git a/tests/golden/config_DTU/nf/allconditions_fastqc-trimgalore-picard-star_DTU_drimseq_subflow.nf b/tests/golden/config_DTU/nf/allconditions_fastqc-trimgalore-picard-star_DTU_drimseq_subflow.nf
index afbb4b21..129f93e8 100644
--- a/tests/golden/config_DTU/nf/allconditions_fastqc-trimgalore-picard-star_DTU_drimseq_subflow.nf
+++ b/tests/golden/config_DTU/nf/allconditions_fastqc-trimgalore-picard-star_DTU_drimseq_subflow.nf
@@ -152,6 +152,25 @@ process salmon_quant{
         """
     }
 }
+process decompress_annotation_dtu{
+    conda "<REPO>/envs/${params.gCOUNTENV}"+".yaml"
+    container "oras://ghcr.io/jfallmann/monsda:"+"${params.gCOUNTENV}"+"-VERSION"
+    cpus 1
+	cache 'lenient'
+    publishDir "${workflow.workDir}/../" , mode: 'link',
+    saveAs: {filename ->
+        if (filename.indexOf("log") > 0)        "LOGS/${params.gSCOMBO}/DTU/"+"${params.gCOUNTENV}"+"/decompress_annotation.log"
+    }
+    input:
+    path anno
+    output:
+    path "annotation.gtf", emit: anno_plain
+    path "log", emit: log
+    script:
+    """
+    zcat -f $anno > annotation.gtf 2> log; if [ ! -s annotation.gtf ]; then echo "ERROR: decompressed annotation from $anno is empty, check source file and filesystem" >> log; exit 1; fi
+    """
+}
 process oarfish_dtu_quant{
     conda "<REPO>/envs/${params.gCOUNTENV}"+".yaml"
     container "oras://ghcr.io/jfallmann/monsda:"+"${params.gCOUNTENV}"+"-VERSION"
@@ -163,18 +182,20 @@ process oarfish_dtu_quant{
         else                                    "DTU/${params.gSCOMBO}/"+"${params.gCOUNTENV}"+"/${params.gCONDITION}/${file(filename).getName()}"
     }
     input:
-    path bam
+    path fls
     output:
     path "*.gz", includeInputs:false, emit: counts
     path "*.log", emit: logs
     script:
+    anno = fls[0]
+    bam = fls[1]
     fn = file(bam).getSimpleName().replaceAll(/\Q_mapped_sorted\E/,"")
     lf = "${params.gCOUNTENV}_"+fn+".log"
     prefix = fn+"/"+params.gCOUNTENV
     oz = fn+"/quant.sf.gz"
     ol = fn+"_counts.gz"
     """
-    mkdir -p $fn; samtools collate -@ ${task.cpus} -o namecollated.bam $bam &>> $lf; zcat -f ${params.gDTUANNO} > $fn/annotation.gtf 2>> $lf; ${params.gCOUNTBIN} --threads ${task.cpus} --genome-alignments namecollated.bam --annotation $fn/annotation.gtf --genome-fasta ${params.gDTUREF} ${params.gCOUNTPARAMS} --output $prefix &>> $lf && rm -f namecollated.bam $fn/annotation.gtf && python3 ${params.gBINS}/Analysis/oarfish_to_salmon.py -i ${prefix}.quant -o $oz &>> $lf && ln -fs $oz $ol
+    mkdir -p $fn; : > $lf; if [ ! -s $anno ]; then echo "ERROR: decompressed annotation $anno is empty, check source file and filesystem" >> $lf; exit 1; fi; samtools collate -@ ${task.cpus} -o namecollated.bam $bam &>> $lf; ${params.gCOUNTBIN} --threads ${task.cpus} --genome-alignments namecollated.bam --annotation $anno --genome-fasta ${params.gDTUREF} ${params.gCOUNTPARAMS} --output $prefix &>> $lf && rm -f namecollated.bam && python3 ${params.gBINS}/Analysis/oarfish_to_salmon.py -i ${prefix}.quant -o $oz &>> $lf && ln -fs $oz $ol
     """
 }
 process create_summary_snippet{
@@ -346,7 +367,9 @@ workflow DTU{
                 element -> return "${workflow.workDir}/../MAPPED/${params.gCOMBO}/"+element+"_mapped_sorted.bam"
             }
         mapsamples_ch = Channel.fromPath(MAPPEDSAMPLES.sort())
-        oarfish_dtu_quant(mapsamples_ch.collate(1))
+        decompress_annotation_dtu(annofile)
+        annogtf_dtu = decompress_annotation_dtu.out.anno_plain
+        oarfish_dtu_quant(annogtf_dtu.combine(mapsamples_ch.collate(1)))
         quantcounts = oarfish_dtu_quant.out.counts
     }
     prepare_dtu_annotation()
diff --git a/tests/golden/config_DTU/nf/allconditions_fastqc-trimgalore-picard-star_DTU_spit_subflow.nf b/tests/golden/config_DTU/nf/allconditions_fastqc-trimgalore-picard-star_DTU_spit_subflow.nf
index 2e0ac723..ccf4b98a 100644
--- a/tests/golden/config_DTU/nf/allconditions_fastqc-trimgalore-picard-star_DTU_spit_subflow.nf
+++ b/tests/golden/config_DTU/nf/allconditions_fastqc-trimgalore-picard-star_DTU_spit_subflow.nf
@@ -152,6 +152,25 @@ process salmon_quant{
         """
     }
 }
+process decompress_annotation_dtu{
+    conda "<REPO>/envs/${params.gCOUNTENV}"+".yaml"
+    container "oras://ghcr.io/jfallmann/monsda:"+"${params.gCOUNTENV}"+"-VERSION"
+    cpus 1
+	cache 'lenient'
+    publishDir "${workflow.workDir}/../" , mode: 'link',
+    saveAs: {filename ->
+        if (filename.indexOf("log") > 0)        "LOGS/${params.gSCOMBO}/DTU/"+"${params.gCOUNTENV}"+"/decompress_annotation.log"
+    }
+    input:
+    path anno
+    output:
+    path "annotation.gtf", emit: anno_plain
+    path "log", emit: log
+    script:
+    """
+    zcat -f $anno > annotation.gtf 2> log; if [ ! -s annotation.gtf ]; then echo "ERROR: decompressed annotation from $anno is empty, check source file and filesystem" >> log; exit 1; fi
+    """
+}
 process oarfish_dtu_quant{
     conda "<REPO>/envs/${params.gCOUNTENV}"+".yaml"
     container "oras://ghcr.io/jfallmann/monsda:"+"${params.gCOUNTENV}"+"-VERSION"
@@ -163,18 +182,20 @@ process oarfish_dtu_quant{
         else                                    "DTU/${params.gSCOMBO}/"+"${params.gCOUNTENV}"+"/${params.gCONDITION}/${file(filename).getName()}"
     }
     input:
-    path bam
+    path fls
     output:
     path "*.gz", includeInputs:false, emit: counts
     path "*.log", emit: logs
     script:
+    anno = fls[0]
+    bam = fls[1]
     fn = file(bam).getSimpleName().replaceAll(/\Q_mapped_sorted\E/,"")
     lf = "${params.gCOUNTENV}_"+fn+".log"
     prefix = fn+"/"+params.gCOUNTENV
     oz = fn+"/quant.sf.gz"
     ol = fn+"_counts.gz"
     """
-    mkdir -p $fn; samtools collate -@ ${task.cpus} -o namecollated.bam $bam &>> $lf; zcat -f ${params.gDTUANNO} > $fn/annotation.gtf 2>> $lf; ${params.gCOUNTBIN} --threads ${task.cpus} --genome-alignments namecollated.bam --annotation $fn/annotation.gtf --genome-fasta ${params.gDTUREF} ${params.gCOUNTPARAMS} --output $prefix &>> $lf && rm -f namecollated.bam $fn/annotation.gtf && python3 ${params.gBINS}/Analysis/oarfish_to_salmon.py -i ${prefix}.quant -o $oz &>> $lf && ln -fs $oz $ol
+    mkdir -p $fn; : > $lf; if [ ! -s $anno ]; then echo "ERROR: decompressed annotation $anno is empty, check source file and filesystem" >> $lf; exit 1; fi; samtools collate -@ ${task.cpus} -o namecollated.bam $bam &>> $lf; ${params.gCOUNTBIN} --threads ${task.cpus} --genome-alignments namecollated.bam --annotation $anno --genome-fasta ${params.gDTUREF} ${params.gCOUNTPARAMS} --output $prefix &>> $lf && rm -f namecollated.bam && python3 ${params.gBINS}/Analysis/oarfish_to_salmon.py -i ${prefix}.quant -o $oz &>> $lf && ln -fs $oz $ol
     """
 }
 process create_summary_snippet{
@@ -344,7 +365,9 @@ workflow DTU{
                 element -> return "${workflow.workDir}/../MAPPED/${params.gCOMBO}/"+element+"_mapped_sorted.bam"
             }
         mapsamples_ch = Channel.fromPath(MAPPEDSAMPLES.sort())
-        oarfish_dtu_quant(mapsamples_ch.collate(1))
+        decompress_annotation_dtu(annofile)
+        annogtf_dtu = decompress_annotation_dtu.out.anno_plain
+        oarfish_dtu_quant(annogtf_dtu.combine(mapsamples_ch.collate(1)))
         quantcounts = oarfish_dtu_quant.out.counts
     }
     prepare_dtu_annotation()
diff --git a/tests/golden/config_DTU/smk/allconditions_fastqc-trimgalore-picard-star_DTU_dexseq_subsnake.smk b/tests/golden/config_DTU/smk/allconditions_fastqc-trimgalore-picard-star_DTU_dexseq_subsnake.smk
index e1aab12d..868fbe7a 100644
--- a/tests/golden/config_DTU/smk/allconditions_fastqc-trimgalore-picard-star_DTU_dexseq_subsnake.smk
+++ b/tests/golden/config_DTU/smk/allconditions_fastqc-trimgalore-picard-star_DTU_dexseq_subsnake.smk
@@ -293,6 +293,10 @@ if 'FUSIONS' in config:
         ANNOTATION = FANNO
     else:
         ANNOTATION = ANNO.get('GTF') if 'GTF' in ANNO and ANNO.get('GTF') != '' else ANNO.get('GFF')  # by default GTF format will be used
+if ANNOTATION and isinstance(ANNOTATION, str):
+    # Resolve once to an absolute path so every rule's shell command can read
+    # it reliably regardless of its own working directory (e.g. containers).
+    ANNOTATION = os.path.abspath(ANNOTATION)
 combo = ''
 if ANNOTATION:
     log.info(logid+f'Using COMBO: {combo}, REF: {REFERENCE}, ANNO: {ANNOTATION}, DECOY: {DECOY}, INDEX: {INDEX}, INDEX2: {INDEX2}, PREFIX: {PREFIX}, IP: {IP}, SETUP: {SETUP}, SEQUENCING: {SEQUENCING}, STRANDED: {stranded}, PAIRED: {paired}, RUNDEDUP: {rundedup}, PREDEDUP: {prededup}, SAMPLES: {SAMPLES}, BINS: {BINS}, MAXTHREAD: {MAXTHREAD}')
@@ -404,9 +408,17 @@ else:
     # is needed, output is normalized to the salmon quant.sf schema so
     # downstream DTU tooling (tximport type="salmon", build_DTU_table.py,
     # SPIT.py) does not need to change.
+    rule decompress_annotation:
+        input:  anno = ANNOTATION
+        output: anno = temp("DTU/{combo}/"+COUNTENV+"/annotation.gtf")
+        log:    "LOGS/{combo}/DTU/"+COUNTENV+"/decompress_annotation.log"
+        conda:  "<REPO>/envs/"+COUNTENV+".yaml"
+        container: "oras://ghcr.io/jfallmann/monsda:"+COUNTENV+""+"-VERSION"
+        threads: 1
+        shell:  "zcat -f {input.anno} > {output.anno} 2> {log}; if [ ! -s {output.anno} ]; then echo 'ERROR: decompressed annotation from {input.anno} is empty, check source file and filesystem' >> {log}; exit 1; fi"
     rule mapping:
         input:  bam = expand("MAPPED/{scombo}/{{file}}_mapped_sorted.bam", scombo=scombo),
-                anno = ANNOTATION,
+                anno = rules.decompress_annotation.output.anno,
                 fa = REFERENCE
         output: cnts = report("DTU/{combo}/"+COUNTENV+"/{file}_counts.sf.gz", category="COUNTING"),
                 ctsdir = report(directory("DTU/{combo}/"+COUNTENV+"/{file}"), category="COUNTING")
@@ -417,11 +429,10 @@ else:
         params: cpara = lambda wildcards: tool_params(wildcards.file, None, config, 'DTU', DTUENV)['OPTIONS'].get('QUANT', ""),
                 mapp = COUNTBIN,
                 nbam = lambda wildcards, output: os.path.join(str(output.ctsdir), "namecollated.bam"),
-                anno = lambda wildcards, output: os.path.join(str(output.ctsdir), "annotation.gtf"),
                 prefix = lambda wildcards, output: os.path.join(str(output.ctsdir), COUNTENV),
                 linksf = lambda wildcards, output: str(os.path.abspath(output.ctsdir)),
                 bins = BINS
-        shell: "set +euo pipefail; mkdir -p {output.ctsdir}; samtools collate -@ {threads} -o {params.nbam} {input.bam} &>> {log}; zcat -f {input.anno} > {params.anno} 2>> {log}; {params.mapp} --threads {threads} --genome-alignments {params.nbam} --annotation {params.anno} --genome-fasta {input.fa} {params.cpara} --output {params.prefix} &>> {log} && rm -f {params.nbam} {params.anno} && python3 {params.bins}/Analysis/oarfish_to_salmon.py -i {params.prefix}.quant -o {output.ctsdir}/quant.sf.gz &>> {log} ; ln -fs {params.linksf}/quant.sf.gz {output.cnts} &>> {log}"
+        shell: "set +euo pipefail; mkdir -p {output.ctsdir}; samtools collate -@ {threads} -o {params.nbam} {input.bam} &>> {log}; {params.mapp} --threads {threads} --genome-alignments {params.nbam} --annotation {input.anno} --genome-fasta {input.fa} {params.cpara} --output {params.prefix} &>> {log} && rm -f {params.nbam} && python3 {params.bins}/Analysis/oarfish_to_salmon.py -i {params.prefix}.quant -o {output.ctsdir}/quant.sf.gz &>> {log} ; ln -fs {params.linksf}/quant.sf.gz {output.cnts} &>> {log}"
 if runterminus:
     rule terminus_group:
         input:  ctsdir = rules.mapping.output.ctsdir
diff --git a/tests/golden/config_DTU/smk/allconditions_fastqc-trimgalore-picard-star_DTU_drimseq_subsnake.smk b/tests/golden/config_DTU/smk/allconditions_fastqc-trimgalore-picard-star_DTU_drimseq_subsnake.smk
index c116c2f3..1cc1c0b5 100644
--- a/tests/golden/config_DTU/smk/allconditions_fastqc-trimgalore-picard-star_DTU_drimseq_subsnake.smk
+++ b/tests/golden/config_DTU/smk/allconditions_fastqc-trimgalore-picard-star_DTU_drimseq_subsnake.smk
@@ -293,6 +293,10 @@ if 'FUSIONS' in config:
         ANNOTATION = FANNO
     else:
         ANNOTATION = ANNO.get('GTF') if 'GTF' in ANNO and ANNO.get('GTF') != '' else ANNO.get('GFF')  # by default GTF format will be used
+if ANNOTATION and isinstance(ANNOTATION, str):
+    # Resolve once to an absolute path so every rule's shell command can read
+    # it reliably regardless of its own working directory (e.g. containers).
+    ANNOTATION = os.path.abspath(ANNOTATION)
 combo = ''
 if ANNOTATION:
     log.info(logid+f'Using COMBO: {combo}, REF: {REFERENCE}, ANNO: {ANNOTATION}, DECOY: {DECOY}, INDEX: {INDEX}, INDEX2: {INDEX2}, PREFIX: {PREFIX}, IP: {IP}, SETUP: {SETUP}, SEQUENCING: {SEQUENCING}, STRANDED: {stranded}, PAIRED: {paired}, RUNDEDUP: {rundedup}, PREDEDUP: {prededup}, SAMPLES: {SAMPLES}, BINS: {BINS}, MAXTHREAD: {MAXTHREAD}')
@@ -414,9 +418,17 @@ else:
     # is needed, output is normalized to the salmon quant.sf schema so
     # downstream DTU tooling (tximport type="salmon", build_DTU_table.py,
     # SPIT.py) does not need to change.
+    rule decompress_annotation:
+        input:  anno = ANNOTATION
+        output: anno = temp("DTU/{combo}/"+COUNTENV+"/annotation.gtf")
+        log:    "LOGS/{combo}/DTU/"+COUNTENV+"/decompress_annotation.log"
+        conda:  "<REPO>/envs/"+COUNTENV+".yaml"
+        container: "oras://ghcr.io/jfallmann/monsda:"+COUNTENV+""+"-VERSION"
+        threads: 1
+        shell:  "zcat -f {input.anno} > {output.anno} 2> {log}; if [ ! -s {output.anno} ]; then echo 'ERROR: decompressed annotation from {input.anno} is empty, check source file and filesystem' >> {log}; exit 1; fi"
     rule mapping:
         input:  bam = expand("MAPPED/{scombo}/{{file}}_mapped_sorted.bam", scombo=scombo),
-                anno = ANNOTATION,
+                anno = rules.decompress_annotation.output.anno,
                 fa = REFERENCE
         output: cnts = report("DTU/{combo}/"+COUNTENV+"/{file}_counts.sf.gz", category="COUNTING"),
                 ctsdir = report(directory("DTU/{combo}/"+COUNTENV+"/{file}"), category="COUNTING")
@@ -427,11 +439,10 @@ else:
         params: cpara = lambda wildcards: tool_params(wildcards.file, None, config, 'DTU', DTUENV)['OPTIONS'].get('QUANT', ""),
                 mapp = COUNTBIN,
                 nbam = lambda wildcards, output: os.path.join(str(output.ctsdir), "namecollated.bam"),
-                anno = lambda wildcards, output: os.path.join(str(output.ctsdir), "annotation.gtf"),
                 prefix = lambda wildcards, output: os.path.join(str(output.ctsdir), COUNTENV),
                 linksf = lambda wildcards, output: str(os.path.abspath(output.ctsdir)),
                 bins = BINS
-        shell: "set +euo pipefail; mkdir -p {output.ctsdir}; samtools collate -@ {threads} -o {params.nbam} {input.bam} &>> {log}; zcat -f {input.anno} > {params.anno} 2>> {log}; {params.mapp} --threads {threads} --genome-alignments {params.nbam} --annotation {params.anno} --genome-fasta {input.fa} {params.cpara} --output {params.prefix} &>> {log} && rm -f {params.nbam} {params.anno} && python3 {params.bins}/Analysis/oarfish_to_salmon.py -i {params.prefix}.quant -o {output.ctsdir}/quant.sf.gz &>> {log} ; ln -fs {params.linksf}/quant.sf.gz {output.cnts} &>> {log}"
+        shell: "set +euo pipefail; mkdir -p {output.ctsdir}; samtools collate -@ {threads} -o {params.nbam} {input.bam} &>> {log}; {params.mapp} --threads {threads} --genome-alignments {params.nbam} --annotation {input.anno} --genome-fasta {input.fa} {params.cpara} --output {params.prefix} &>> {log} && rm -f {params.nbam} && python3 {params.bins}/Analysis/oarfish_to_salmon.py -i {params.prefix}.quant -o {output.ctsdir}/quant.sf.gz &>> {log} ; ln -fs {params.linksf}/quant.sf.gz {output.cnts} &>> {log}"
 if runterminus:
     rule terminus_group:
         input:  ctsdir = rules.mapping.output.ctsdir
diff --git a/tests/golden/config_DTU/smk/allconditions_fastqc-trimgalore-picard-star_DTU_spit_subsnake.smk b/tests/golden/config_DTU/smk/allconditions_fastqc-trimgalore-picard-star_DTU_spit_subsnake.smk
index 9e592ea8..4c4f8440 100644
--- a/tests/golden/config_DTU/smk/allconditions_fastqc-trimgalore-picard-star_DTU_spit_subsnake.smk
+++ b/tests/golden/config_DTU/smk/allconditions_fastqc-trimgalore-picard-star_DTU_spit_subsnake.smk
@@ -293,6 +293,10 @@ if 'FUSIONS' in config:
         ANNOTATION = FANNO
     else:
         ANNOTATION = ANNO.get('GTF') if 'GTF' in ANNO and ANNO.get('GTF') != '' else ANNO.get('GFF')  # by default GTF format will be used
+if ANNOTATION and isinstance(ANNOTATION, str):
+    # Resolve once to an absolute path so every rule's shell command can read
+    # it reliably regardless of its own working directory (e.g. containers).
+    ANNOTATION = os.path.abspath(ANNOTATION)
 combo = ''
 if ANNOTATION:
     log.info(logid+f'Using COMBO: {combo}, REF: {REFERENCE}, ANNO: {ANNOTATION}, DECOY: {DECOY}, INDEX: {INDEX}, INDEX2: {INDEX2}, PREFIX: {PREFIX}, IP: {IP}, SETUP: {SETUP}, SEQUENCING: {SEQUENCING}, STRANDED: {stranded}, PAIRED: {paired}, RUNDEDUP: {rundedup}, PREDEDUP: {prededup}, SAMPLES: {SAMPLES}, BINS: {BINS}, MAXTHREAD: {MAXTHREAD}')
@@ -411,9 +415,17 @@ else:
     # is needed, output is normalized to the salmon quant.sf schema so
     # downstream DTU tooling (tximport type="salmon", build_DTU_table.py,
     # SPIT.py) does not need to change.
+    rule decompress_annotation:
+        input:  anno = ANNOTATION
+        output: anno = temp("DTU/{combo}/"+COUNTENV+"/annotation.gtf")
+        log:    "LOGS/{combo}/DTU/"+COUNTENV+"/decompress_annotation.log"
+        conda:  "<REPO>/envs/"+COUNTENV+".yaml"
+        container: "oras://ghcr.io/jfallmann/monsda:"+COUNTENV+""+"-VERSION"
+        threads: 1
+        shell:  "zcat -f {input.anno} > {output.anno} 2> {log}; if [ ! -s {output.anno} ]; then echo 'ERROR: decompressed annotation from {input.anno} is empty, check source file and filesystem' >> {log}; exit 1; fi"
     rule mapping:
         input:  bam = expand("MAPPED/{scombo}/{{file}}_mapped_sorted.bam", scombo=scombo),
-                anno = ANNOTATION,
+                anno = rules.decompress_annotation.output.anno,
                 fa = REFERENCE
         output: cnts = report("DTU/{combo}/"+COUNTENV+"/{file}_counts.sf.gz", category="COUNTING"),
                 ctsdir = report(directory("DTU/{combo}/"+COUNTENV+"/{file}"), category="COUNTING")
@@ -424,11 +436,10 @@ else:
         params: cpara = lambda wildcards: tool_params(wildcards.file, None, config, 'DTU', DTUENV)['OPTIONS'].get('QUANT', ""),
                 mapp = COUNTBIN,
                 nbam = lambda wildcards, output: os.path.join(str(output.ctsdir), "namecollated.bam"),
-                anno = lambda wildcards, output: os.path.join(str(output.ctsdir), "annotation.gtf"),
                 prefix = lambda wildcards, output: os.path.join(str(output.ctsdir), COUNTENV),
                 linksf = lambda wildcards, output: str(os.path.abspath(output.ctsdir)),
                 bins = BINS
-        shell: "set +euo pipefail; mkdir -p {output.ctsdir}; samtools collate -@ {threads} -o {params.nbam} {input.bam} &>> {log}; zcat -f {input.anno} > {params.anno} 2>> {log}; {params.mapp} --threads {threads} --genome-alignments {params.nbam} --annotation {params.anno} --genome-fasta {input.fa} {params.cpara} --output {params.prefix} &>> {log} && rm -f {params.nbam} {params.anno} && python3 {params.bins}/Analysis/oarfish_to_salmon.py -i {params.prefix}.quant -o {output.ctsdir}/quant.sf.gz &>> {log} ; ln -fs {params.linksf}/quant.sf.gz {output.cnts} &>> {log}"
+        shell: "set +euo pipefail; mkdir -p {output.ctsdir}; samtools collate -@ {threads} -o {params.nbam} {input.bam} &>> {log}; {params.mapp} --threads {threads} --genome-alignments {params.nbam} --annotation {input.anno} --genome-fasta {input.fa} {params.cpara} --output {params.prefix} &>> {log} && rm -f {params.nbam} && python3 {params.bins}/Analysis/oarfish_to_salmon.py -i {params.prefix}.quant -o {output.ctsdir}/quant.sf.gz &>> {log} ; ln -fs {params.linksf}/quant.sf.gz {output.cnts} &>> {log}"
 if runterminus:
     rule terminus_group:
         input:  ctsdir = rules.mapping.output.ctsdir
diff --git a/tests/golden/config_FUSIONS/smk/allconditions_fastqc-trimgalore-picard-star_FUSIONS_starfusion_subsnake.smk b/tests/golden/config_FUSIONS/smk/allconditions_fastqc-trimgalore-picard-star_FUSIONS_starfusion_subsnake.smk
index cde1eadf..6aba6a5b 100644
--- a/tests/golden/config_FUSIONS/smk/allconditions_fastqc-trimgalore-picard-star_FUSIONS_starfusion_subsnake.smk
+++ b/tests/golden/config_FUSIONS/smk/allconditions_fastqc-trimgalore-picard-star_FUSIONS_starfusion_subsnake.smk
@@ -293,6 +293,10 @@ if 'FUSIONS' in config:
         ANNOTATION = FANNO
     else:
         ANNOTATION = ANNO.get('GTF') if 'GTF' in ANNO and ANNO.get('GTF') != '' else ANNO.get('GFF')  # by default GTF format will be used
+if ANNOTATION and isinstance(ANNOTATION, str):
+    # Resolve once to an absolute path so every rule's shell command can read
+    # it reliably regardless of its own working directory (e.g. containers).
+    ANNOTATION = os.path.abspath(ANNOTATION)
 combo = ''
 if ANNOTATION:
     log.info(logid+f'Using COMBO: {combo}, REF: {REFERENCE}, ANNO: {ANNOTATION}, DECOY: {DECOY}, INDEX: {INDEX}, INDEX2: {INDEX2}, PREFIX: {PREFIX}, IP: {IP}, SETUP: {SETUP}, SEQUENCING: {SEQUENCING}, STRANDED: {stranded}, PAIRED: {paired}, RUNDEDUP: {rundedup}, PREDEDUP: {prededup}, SAMPLES: {SAMPLES}, BINS: {BINS}, MAXTHREAD: {MAXTHREAD}')
diff --git a/tests/golden/config_Test/smk/Test_fastqc-bbduk-picard-bwa_subsnake.smk b/tests/golden/config_Test/smk/Test_fastqc-bbduk-picard-bwa_subsnake.smk
index 7d78489f..f30e41e7 100644
--- a/tests/golden/config_Test/smk/Test_fastqc-bbduk-picard-bwa_subsnake.smk
+++ b/tests/golden/config_Test/smk/Test_fastqc-bbduk-picard-bwa_subsnake.smk
@@ -293,6 +293,10 @@ if 'FUSIONS' in config:
         ANNOTATION = FANNO
     else:
         ANNOTATION = ANNO.get('GTF') if 'GTF' in ANNO and ANNO.get('GTF') != '' else ANNO.get('GFF')  # by default GTF format will be used
+if ANNOTATION and isinstance(ANNOTATION, str):
+    # Resolve once to an absolute path so every rule's shell command can read
+    # it reliably regardless of its own working directory (e.g. containers).
+    ANNOTATION = os.path.abspath(ANNOTATION)
 combo = ''
 if ANNOTATION:
     log.info(logid+f'Using COMBO: {combo}, REF: {REFERENCE}, ANNO: {ANNOTATION}, DECOY: {DECOY}, INDEX: {INDEX}, INDEX2: {INDEX2}, PREFIX: {PREFIX}, IP: {IP}, SETUP: {SETUP}, SEQUENCING: {SEQUENCING}, STRANDED: {stranded}, PAIRED: {paired}, RUNDEDUP: {rundedup}, PREDEDUP: {prededup}, SAMPLES: {SAMPLES}, BINS: {BINS}, MAXTHREAD: {MAXTHREAD}')
diff --git a/tests/golden/config_Test/smk/Test_fastqc-bbduk-picard-rustar_subsnake.smk b/tests/golden/config_Test/smk/Test_fastqc-bbduk-picard-rustar_subsnake.smk
index e6c2b076..de09320b 100644
--- a/tests/golden/config_Test/smk/Test_fastqc-bbduk-picard-rustar_subsnake.smk
+++ b/tests/golden/config_Test/smk/Test_fastqc-bbduk-picard-rustar_subsnake.smk
@@ -293,6 +293,10 @@ if 'FUSIONS' in config:
         ANNOTATION = FANNO
     else:
         ANNOTATION = ANNO.get('GTF') if 'GTF' in ANNO and ANNO.get('GTF') != '' else ANNO.get('GFF')  # by default GTF format will be used
+if ANNOTATION and isinstance(ANNOTATION, str):
+    # Resolve once to an absolute path so every rule's shell command can read
+    # it reliably regardless of its own working directory (e.g. containers).
+    ANNOTATION = os.path.abspath(ANNOTATION)
 combo = ''
 if ANNOTATION:
     log.info(logid+f'Using COMBO: {combo}, REF: {REFERENCE}, ANNO: {ANNOTATION}, DECOY: {DECOY}, INDEX: {INDEX}, INDEX2: {INDEX2}, PREFIX: {PREFIX}, IP: {IP}, SETUP: {SETUP}, SEQUENCING: {SEQUENCING}, STRANDED: {stranded}, PAIRED: {paired}, RUNDEDUP: {rundedup}, PREDEDUP: {prededup}, SAMPLES: {SAMPLES}, BINS: {BINS}, MAXTHREAD: {MAXTHREAD}')
diff --git a/tests/golden/config_Test/smk/Test_fastqc-bbduk-picard-star_subsnake.smk b/tests/golden/config_Test/smk/Test_fastqc-bbduk-picard-star_subsnake.smk
index a97ad49a..b80e8001 100644
--- a/tests/golden/config_Test/smk/Test_fastqc-bbduk-picard-star_subsnake.smk
+++ b/tests/golden/config_Test/smk/Test_fastqc-bbduk-picard-star_subsnake.smk
@@ -293,6 +293,10 @@ if 'FUSIONS' in config:
         ANNOTATION = FANNO
     else:
         ANNOTATION = ANNO.get('GTF') if 'GTF' in ANNO and ANNO.get('GTF') != '' else ANNO.get('GFF')  # by default GTF format will be used
+if ANNOTATION and isinstance(ANNOTATION, str):
+    # Resolve once to an absolute path so every rule's shell command can read
+    # it reliably regardless of its own working directory (e.g. containers).
+    ANNOTATION = os.path.abspath(ANNOTATION)
 combo = ''
 if ANNOTATION:
     log.info(logid+f'Using COMBO: {combo}, REF: {REFERENCE}, ANNO: {ANNOTATION}, DECOY: {DECOY}, INDEX: {INDEX}, INDEX2: {INDEX2}, PREFIX: {PREFIX}, IP: {IP}, SETUP: {SETUP}, SEQUENCING: {SEQUENCING}, STRANDED: {stranded}, PAIRED: {paired}, RUNDEDUP: {rundedup}, PREDEDUP: {prededup}, SAMPLES: {SAMPLES}, BINS: {BINS}, MAXTHREAD: {MAXTHREAD}')
diff --git a/tests/golden/config_Test/smk/Test_fastqc-cutadapt-picard-bwa_subsnake.smk b/tests/golden/config_Test/smk/Test_fastqc-cutadapt-picard-bwa_subsnake.smk
index c75b659a..c77aa534 100644
--- a/tests/golden/config_Test/smk/Test_fastqc-cutadapt-picard-bwa_subsnake.smk
+++ b/tests/golden/config_Test/smk/Test_fastqc-cutadapt-picard-bwa_subsnake.smk
@@ -293,6 +293,10 @@ if 'FUSIONS' in config:
         ANNOTATION = FANNO
     else:
         ANNOTATION = ANNO.get('GTF') if 'GTF' in ANNO and ANNO.get('GTF') != '' else ANNO.get('GFF')  # by default GTF format will be used
+if ANNOTATION and isinstance(ANNOTATION, str):
+    # Resolve once to an absolute path so every rule's shell command can read
+    # it reliably regardless of its own working directory (e.g. containers).
+    ANNOTATION = os.path.abspath(ANNOTATION)
 combo = ''
 if ANNOTATION:
     log.info(logid+f'Using COMBO: {combo}, REF: {REFERENCE}, ANNO: {ANNOTATION}, DECOY: {DECOY}, INDEX: {INDEX}, INDEX2: {INDEX2}, PREFIX: {PREFIX}, IP: {IP}, SETUP: {SETUP}, SEQUENCING: {SEQUENCING}, STRANDED: {stranded}, PAIRED: {paired}, RUNDEDUP: {rundedup}, PREDEDUP: {prededup}, SAMPLES: {SAMPLES}, BINS: {BINS}, MAXTHREAD: {MAXTHREAD}')
diff --git a/tests/golden/config_Test/smk/Test_fastqc-cutadapt-picard-rustar_subsnake.smk b/tests/golden/config_Test/smk/Test_fastqc-cutadapt-picard-rustar_subsnake.smk
index f630ccd6..15ec53d0 100644
--- a/tests/golden/config_Test/smk/Test_fastqc-cutadapt-picard-rustar_subsnake.smk
+++ b/tests/golden/config_Test/smk/Test_fastqc-cutadapt-picard-rustar_subsnake.smk
@@ -293,6 +293,10 @@ if 'FUSIONS' in config:
         ANNOTATION = FANNO
     else:
         ANNOTATION = ANNO.get('GTF') if 'GTF' in ANNO and ANNO.get('GTF') != '' else ANNO.get('GFF')  # by default GTF format will be used
+if ANNOTATION and isinstance(ANNOTATION, str):
+    # Resolve once to an absolute path so every rule's shell command can read
+    # it reliably regardless of its own working directory (e.g. containers).
+    ANNOTATION = os.path.abspath(ANNOTATION)
 combo = ''
 if ANNOTATION:
     log.info(logid+f'Using COMBO: {combo}, REF: {REFERENCE}, ANNO: {ANNOTATION}, DECOY: {DECOY}, INDEX: {INDEX}, INDEX2: {INDEX2}, PREFIX: {PREFIX}, IP: {IP}, SETUP: {SETUP}, SEQUENCING: {SEQUENCING}, STRANDED: {stranded}, PAIRED: {paired}, RUNDEDUP: {rundedup}, PREDEDUP: {prededup}, SAMPLES: {SAMPLES}, BINS: {BINS}, MAXTHREAD: {MAXTHREAD}')
diff --git a/tests/golden/config_Test/smk/Test_fastqc-cutadapt-picard-star_subsnake.smk b/tests/golden/config_Test/smk/Test_fastqc-cutadapt-picard-star_subsnake.smk
index 8048518c..af644e01 100644
--- a/tests/golden/config_Test/smk/Test_fastqc-cutadapt-picard-star_subsnake.smk
+++ b/tests/golden/config_Test/smk/Test_fastqc-cutadapt-picard-star_subsnake.smk
@@ -293,6 +293,10 @@ if 'FUSIONS' in config:
         ANNOTATION = FANNO
     else:
         ANNOTATION = ANNO.get('GTF') if 'GTF' in ANNO and ANNO.get('GTF') != '' else ANNO.get('GFF')  # by default GTF format will be used
+if ANNOTATION and isinstance(ANNOTATION, str):
+    # Resolve once to an absolute path so every rule's shell command can read
+    # it reliably regardless of its own working directory (e.g. containers).
+    ANNOTATION = os.path.abspath(ANNOTATION)
 combo = ''
 if ANNOTATION:
     log.info(logid+f'Using COMBO: {combo}, REF: {REFERENCE}, ANNO: {ANNOTATION}, DECOY: {DECOY}, INDEX: {INDEX}, INDEX2: {INDEX2}, PREFIX: {PREFIX}, IP: {IP}, SETUP: {SETUP}, SEQUENCING: {SEQUENCING}, STRANDED: {stranded}, PAIRED: {paired}, RUNDEDUP: {rundedup}, PREDEDUP: {prededup}, SAMPLES: {SAMPLES}, BINS: {BINS}, MAXTHREAD: {MAXTHREAD}')
diff --git a/tests/golden/config_Test/smk/Test_fastqc-trimgalore-picard-bwa_subsnake.smk b/tests/golden/config_Test/smk/Test_fastqc-trimgalore-picard-bwa_subsnake.smk
index c31378a3..514ac158 100644
--- a/tests/golden/config_Test/smk/Test_fastqc-trimgalore-picard-bwa_subsnake.smk
+++ b/tests/golden/config_Test/smk/Test_fastqc-trimgalore-picard-bwa_subsnake.smk
@@ -293,6 +293,10 @@ if 'FUSIONS' in config:
         ANNOTATION = FANNO
     else:
         ANNOTATION = ANNO.get('GTF') if 'GTF' in ANNO and ANNO.get('GTF') != '' else ANNO.get('GFF')  # by default GTF format will be used
+if ANNOTATION and isinstance(ANNOTATION, str):
+    # Resolve once to an absolute path so every rule's shell command can read
+    # it reliably regardless of its own working directory (e.g. containers).
+    ANNOTATION = os.path.abspath(ANNOTATION)
 combo = ''
 if ANNOTATION:
     log.info(logid+f'Using COMBO: {combo}, REF: {REFERENCE}, ANNO: {ANNOTATION}, DECOY: {DECOY}, INDEX: {INDEX}, INDEX2: {INDEX2}, PREFIX: {PREFIX}, IP: {IP}, SETUP: {SETUP}, SEQUENCING: {SEQUENCING}, STRANDED: {stranded}, PAIRED: {paired}, RUNDEDUP: {rundedup}, PREDEDUP: {prededup}, SAMPLES: {SAMPLES}, BINS: {BINS}, MAXTHREAD: {MAXTHREAD}')
diff --git a/tests/golden/config_Test/smk/Test_fastqc-trimgalore-picard-rustar_subsnake.smk b/tests/golden/config_Test/smk/Test_fastqc-trimgalore-picard-rustar_subsnake.smk
index 3c0358ab..7ba6f00f 100644
--- a/tests/golden/config_Test/smk/Test_fastqc-trimgalore-picard-rustar_subsnake.smk
+++ b/tests/golden/config_Test/smk/Test_fastqc-trimgalore-picard-rustar_subsnake.smk
@@ -293,6 +293,10 @@ if 'FUSIONS' in config:
         ANNOTATION = FANNO
     else:
         ANNOTATION = ANNO.get('GTF') if 'GTF' in ANNO and ANNO.get('GTF') != '' else ANNO.get('GFF')  # by default GTF format will be used
+if ANNOTATION and isinstance(ANNOTATION, str):
+    # Resolve once to an absolute path so every rule's shell command can read
+    # it reliably regardless of its own working directory (e.g. containers).
+    ANNOTATION = os.path.abspath(ANNOTATION)
 combo = ''
 if ANNOTATION:
     log.info(logid+f'Using COMBO: {combo}, REF: {REFERENCE}, ANNO: {ANNOTATION}, DECOY: {DECOY}, INDEX: {INDEX}, INDEX2: {INDEX2}, PREFIX: {PREFIX}, IP: {IP}, SETUP: {SETUP}, SEQUENCING: {SEQUENCING}, STRANDED: {stranded}, PAIRED: {paired}, RUNDEDUP: {rundedup}, PREDEDUP: {prededup}, SAMPLES: {SAMPLES}, BINS: {BINS}, MAXTHREAD: {MAXTHREAD}')
diff --git a/tests/golden/config_Test/smk/Test_fastqc-trimgalore-picard-star_subsnake.smk b/tests/golden/config_Test/smk/Test_fastqc-trimgalore-picard-star_subsnake.smk
index e336b7fe..800e9ebd 100644
--- a/tests/golden/config_Test/smk/Test_fastqc-trimgalore-picard-star_subsnake.smk
+++ b/tests/golden/config_Test/smk/Test_fastqc-trimgalore-picard-star_subsnake.smk
@@ -293,6 +293,10 @@ if 'FUSIONS' in config:
         ANNOTATION = FANNO
     else:
         ANNOTATION = ANNO.get('GTF') if 'GTF' in ANNO and ANNO.get('GTF') != '' else ANNO.get('GFF')  # by default GTF format will be used
+if ANNOTATION and isinstance(ANNOTATION, str):
+    # Resolve once to an absolute path so every rule's shell command can read
+    # it reliably regardless of its own working directory (e.g. containers).
+    ANNOTATION = os.path.abspath(ANNOTATION)
 combo = ''
 if ANNOTATION:
     log.info(logid+f'Using COMBO: {combo}, REF: {REFERENCE}, ANNO: {ANNOTATION}, DECOY: {DECOY}, INDEX: {INDEX}, INDEX2: {INDEX2}, PREFIX: {PREFIX}, IP: {IP}, SETUP: {SETUP}, SEQUENCING: {SEQUENCING}, STRANDED: {stranded}, PAIRED: {paired}, RUNDEDUP: {rundedup}, PREDEDUP: {prededup}, SAMPLES: {SAMPLES}, BINS: {BINS}, MAXTHREAD: {MAXTHREAD}')
diff --git a/workflows/deseq2_DE.nf b/workflows/deseq2_DE.nf
index f15d570c..3f1e9c13 100644
--- a/workflows/deseq2_DE.nf
+++ b/workflows/deseq2_DE.nf
@@ -24,6 +24,30 @@ QUANTPARAMS = get_always('deseq2_DE_params_QUANT') ?: ''
 
 //DE PROCESSES
 
+process decompress_annotation_deseq{
+    conda "$COUNTENV"+".yaml"
+    container "oras://jfallmann/monsda:"+"$COUNTENV"
+    cpus 1
+	cache 'lenient'
+
+    publishDir "${workflow.workDir}/../" , mode: 'link',
+    saveAs: {filename ->
+        if (filename.indexOf("log") > 0)        "LOGS/${SCOMBO}/DE/deseq2/decompress_annotation.log"
+    }
+
+    input:
+    path anno
+
+    output:
+    path "annotation.gtf", emit: anno_plain
+    path "log", emit: log
+
+    script:
+    """
+    zcat -f $anno > annotation.gtf 2> log; if [ ! -s annotation.gtf ]; then echo "ERROR: decompressed annotation from $anno is empty, check source file and filesystem" >> log; exit 1; fi
+    """
+}
+
 process featurecount_deseq{
     conda "$COUNTENV"+".yaml"
     container "oras://jfallmann/monsda:"+"$COUNTENV"
@@ -69,7 +93,7 @@ process featurecount_deseq{
             stranded = ''
     }
     """
-    mkdir -p TMP; zcat -f $anno > annotation.gtf 2> $ol; $COUNTBIN -T ${task.cpus} $COUNTPARAMS $pair $stranded -a annotation.gtf -o tmpcts $reads 2>> $ol && rm -f annotation.gtf && head -n2 tmpcts |gzip > $oc && export LC_ALL=C; tail -n+3 tmpcts|sort --parallel=${task.cpus} -S $sortmem -T TMP -k1,1 -k2,2n -k3,3n -u |gzip >> $oc 2>> $ol && mv tmpcts.summary $os
+    mkdir -p TMP; : > $ol; if [ ! -s $anno ]; then echo "ERROR: decompressed annotation $anno is empty, check source file and filesystem" >> $ol; exit 1; fi; $COUNTBIN -T ${task.cpus} $COUNTPARAMS $pair $stranded -a $anno -o tmpcts $reads 2>> $ol && head -n2 tmpcts |gzip > $oc && export LC_ALL=C; tail -n+3 tmpcts|sort --parallel=${task.cpus} -S $sortmem -T TMP -k1,1 -k2,2n -k3,3n -u |gzip >> $oc 2>> $ol && mv tmpcts.summary $os
     """
 }
 
@@ -103,7 +127,7 @@ process oarfish_gene_count{
     os = fn+".counts.summary"
     ol = fn+".log"
     """
-    samtools collate -@ ${task.cpus} -o namecollated.bam $bam &>> $ol; zcat -f $anno > annotation.gtf 2>> $ol; $COUNTBIN --threads ${task.cpus} --genome-alignments namecollated.bam --annotation annotation.gtf --genome-fasta $DEREF $QUANTPARAMS --output $fn &>> $ol && rm -f namecollated.bam annotation.gtf && python3 $BINS/Analysis/oarfish_to_featurecounts.py -i ${fn}.quant -g $anno -s ${fn}_mapped_sorted.bam -o $oc 2>> $ol && touch $os
+    : > $ol; if [ ! -s $anno ]; then echo "ERROR: decompressed annotation $anno is empty, check source file and filesystem" >> $ol; exit 1; fi; samtools collate -@ ${task.cpus} -o namecollated.bam $bam &>> $ol; $COUNTBIN --threads ${task.cpus} --genome-alignments namecollated.bam --annotation $anno --genome-fasta $DEREF $QUANTPARAMS --output $fn &>> $ol && rm -f namecollated.bam && python3 $BINS/Analysis/oarfish_to_featurecounts.py -i ${fn}.quant -g $anno -s ${fn}_mapped_sorted.bam -o $oc 2>> $ol && touch $os
     """
 }
 
@@ -282,6 +306,9 @@ workflow DE{
     
     annofile = Channel.fromPath(DEANNO)
 
+    decompress_annotation_deseq(annofile)
+    annogtf = decompress_annotation_deseq.out.anno_plain
+
     if (COUNTTOOL == 'featureCounts'){
         if (RUNDEDUP){
             MAPPEDSAMPLES = LONGSAMPLES.collect{
@@ -296,7 +323,7 @@ workflow DE{
         mapsamples_ch = Channel.fromPath(MAPPEDSAMPLES.sort())
         //mapsamples_ch.subscribe {  println "MAP: $it \t COMBO: ${COMBO} SCOMBO: ${SCOMBO} LONG: ${LONGSAMPLES}"  }
 
-        featurecount_deseq(annofile.combine(mapsamples_ch.collate(1)))
+        featurecount_deseq(annogtf.combine(mapsamples_ch.collate(1)))
         countcts = featurecount_deseq.out.fc_cts
     }else{
         MAPPEDSAMPLES = LONGSAMPLES.collect{
@@ -304,7 +331,7 @@ workflow DE{
         }
         mapsamples_ch = Channel.fromPath(MAPPEDSAMPLES.sort())
 
-        oarfish_gene_count(annofile.combine(mapsamples_ch.collate(1)))
+        oarfish_gene_count(annogtf.combine(mapsamples_ch.collate(1)))
         countcts = oarfish_gene_count.out.fc_cts
     }
 
diff --git a/workflows/deseq2_DE.smk b/workflows/deseq2_DE.smk
index 296d55db..2d48f6da 100644
--- a/workflows/deseq2_DE.smk
+++ b/workflows/deseq2_DE.smk
@@ -30,9 +30,19 @@ rule themall:
             Rmd = expand("REPORTS/SUMMARY/RmdSnippets/{combo}.Rmd", combo=combo),
             postde = expand("POSTDE/{combo}", combo=combo) if postde_enabled else []
 
+rule decompress_annotation:
+    input:  anno = ANNOTATION
+    output: anno = temp("DE/{combo}/Featurecounts/annotation.gtf")
+    log:    "LOGS/{combo}/DE/deseq2/decompress_annotation.log"
+    conda:  ""+COUNTENV+".yaml"
+    container: "oras://jfallmann/monsda:"+COUNTENV+""
+    threads: 1
+    shell:  "zcat -f {input.anno} > {output.anno} 2> {log}; if [ ! -s {output.anno} ]; then echo 'ERROR: decompressed annotation from {input.anno} is empty, check source file and filesystem' >> {log}; exit 1; fi"
+
 if COUNTTOOL == 'featureCounts':
     rule featurecount_unique:
-        input:  reads = expand("MAPPED/{scombo}/{{file}}_mapped_sorted_unique.bam", scombo=scombo) if not usededup else expand("MAPPED/{scombo}/{{file}}_mapped_sorted_unique_dedup.bam", scombo=scombo)
+        input:  reads = expand("MAPPED/{scombo}/{{file}}_mapped_sorted_unique.bam", scombo=scombo) if not usededup else expand("MAPPED/{scombo}/{{file}}_mapped_sorted_unique_dedup.bam", scombo=scombo),
+                anno  = rules.decompress_annotation.output.anno
         output: tmp   = temp("DE/{combo}/Featurecounts/{file}_tmp.counts"),
                 tmph  = temp("DE/{combo}/Featurecounts/{file}_tmp.head.gz"),
                 tmpc  = temp("DE/{combo}/Featurecounts/{file}_tmp.count.gz"),
@@ -42,30 +52,30 @@ if COUNTTOOL == 'featureCounts':
         container: "oras://jfallmann/monsda:"+COUNTENV+""
         threads: MAXTHREAD
         params: countb = COUNTBIN,
-                anno = ANNOTATION,
                 cpara = lambda wildcards: tool_params(wildcards.file, None, config, "DE", DEENV.split('_')[0])['OPTIONS'].get('COUNT', ""),
                 paired   = lambda x: '-p' if paired == 'paired' else '',
                 stranded = lambda x: '-s 1' if stranded == 'fr' else '-s 2' if stranded == 'rf' else '',
                 sortmem = get_sortmem,
                 prefix = lambda wildcards: "DE/"+combo+"/Featurecounts/"+wildcards.file
-        shell:  "mkdir -p $(dirname {params.prefix}); zcat -f {params.anno} > {params.prefix}_annotation.gtf 2> {log}; {params.countb} -T {threads} {params.cpara} {params.paired} {params.stranded} -a {params.prefix}_annotation.gtf -o {output.tmp} {input.reads} 2>> {log} && rm -f {params.prefix}_annotation.gtf && head -n2 {output.tmp} |gzip > {output.tmph} && export LC_ALL=C; tail -n+3 {output.tmp}|sort --parallel={threads} -S {params.sortmem}G -T TMP -k1,1 -k2,2n -k3,3n -u |gzip >> {output.tmpc} && zcat {output.tmph} {output.tmpc} |gzip > {output.cts} && mv {output.tmp}.summary {output.cts}.summary"
+        shell:  "mkdir -p $(dirname {params.prefix}); {params.countb} -T {threads} {params.cpara} {params.paired} {params.stranded} -a {input.anno} -o {output.tmp} {input.reads} 2> {log} && head -n2 {output.tmp} |gzip > {output.tmph} && export LC_ALL=C; tail -n+3 {output.tmp}|sort --parallel={threads} -S {params.sortmem}G -T TMP -k1,1 -k2,2n -k3,3n -u |gzip >> {output.tmpc} && zcat {output.tmph} {output.tmpc} |gzip > {output.cts} && mv {output.tmp}.summary {output.cts}.summary"
 else:
     # Long-read quantifiers (e.g. oarfish) quantify directly from the
     # genome-mapped BAM and are aggregated to gene level afterwards.
     rule featurecount_unique:
-        input:  reads = expand("MAPPED/{scombo}/{{file}}_mapped_sorted.bam", scombo=scombo)
+        input:  reads = expand("MAPPED/{scombo}/{{file}}_mapped_sorted.bam", scombo=scombo),
+                anno  = rules.decompress_annotation.output.anno
         output: cts   = "DE/{combo}/Featurecounts/{file}_mapped_sorted_unique.counts.gz" if not usededup else "DE/{combo}/Featurecounts/{file}_mapped_sorted_unique_dedup.counts.gz"
         log:    "LOGS/{combo}/{file}/DE/deseq2/"+COUNTENV+"_deseq2_unique.log"
         conda:  ""+COUNTENV+".yaml"
         container: "oras://jfallmann/monsda:"+COUNTENV+""
         threads: MAXTHREAD
         params: countb = COUNTBIN,
-                anno = ANNOTATION,
+                origanno = ANNOTATION,
                 ref = REFERENCE,
                 cpara = lambda wildcards: tool_params(wildcards.file, None, config, "DE", DEENV.split('_')[0])['OPTIONS'].get('QUANT', ""),
                 bins = BINS,
                 prefix = lambda wildcards: "DE/"+combo+"/Featurecounts/"+wildcards.file
-        shell:  "mkdir -p $(dirname {params.prefix}); samtools collate -@ {threads} -o {params.prefix}_namecollated.bam {input.reads} 2> {log}; zcat -f {params.anno} > {params.prefix}_annotation.gtf 2>> {log}; {params.countb} --threads {threads} --genome-alignments {params.prefix}_namecollated.bam --annotation {params.prefix}_annotation.gtf --genome-fasta {params.ref} {params.cpara} --output {params.prefix} 2>> {log} && rm -f {params.prefix}_namecollated.bam {params.prefix}_annotation.gtf && python3 {params.bins}/Analysis/oarfish_to_featurecounts.py -i {params.prefix}.quant -g {params.anno} -s {wildcards.file}_mapped_sorted.bam -o {output.cts} 2>> {log}"
+        shell:  "mkdir -p $(dirname {params.prefix}); samtools collate -@ {threads} -o {params.prefix}_namecollated.bam {input.reads} 2> {log}; {params.countb} --threads {threads} --genome-alignments {params.prefix}_namecollated.bam --annotation {input.anno} --genome-fasta {params.ref} {params.cpara} --output {params.prefix} 2>> {log} && rm -f {params.prefix}_namecollated.bam && python3 {params.bins}/Analysis/oarfish_to_featurecounts.py -i {params.prefix}.quant -g {params.origanno} -s {wildcards.file}_mapped_sorted.bam -o {output.cts} 2>> {log}"
 
 rule prepare_count_table:
     input:   cnd  = expand(rules.featurecount_unique.output.cts, combo=combo, file=samplecond(SAMPLES, config))
diff --git a/workflows/dexseq_DTU.nf b/workflows/dexseq_DTU.nf
index 33f0e7d0..7e268524 100644
--- a/workflows/dexseq_DTU.nf
+++ b/workflows/dexseq_DTU.nf
@@ -27,7 +27,7 @@ PCOMBO = get_always('COMBO') ?: 'none'
 
 //DTU PROCESSES
 
-include { salmon_quant; oarfish_dtu_quant; create_summary_snippet; terminus_collapse } from "dtu_base.nf"
+include { salmon_quant; decompress_annotation_dtu; oarfish_dtu_quant; create_summary_snippet; terminus_collapse } from "dtu_base.nf"
 
 process salmon_idx{
     conda "$COUNTENV"+".yaml"
@@ -182,7 +182,9 @@ workflow DTU{
                 element -> return "${workflow.workDir}/../MAPPED/${COMBO}/"+element+"_mapped_sorted.bam"
             }
         mapsamples_ch = Channel.fromPath(MAPPEDSAMPLES.sort())
-        oarfish_dtu_quant(mapsamples_ch.collate(1))
+        decompress_annotation_dtu(annofile)
+        annogtf_dtu = decompress_annotation_dtu.out.anno_plain
+        oarfish_dtu_quant(annogtf_dtu.combine(mapsamples_ch.collate(1)))
         quantcounts = oarfish_dtu_quant.out.counts
     }
 
diff --git a/workflows/drimseq_DTU.nf b/workflows/drimseq_DTU.nf
index 89cabc59..bad83c5e 100644
--- a/workflows/drimseq_DTU.nf
+++ b/workflows/drimseq_DTU.nf
@@ -27,7 +27,7 @@ PCOMBO = get_always('COMBO') ?: 'none'
 
 //DTU PROCESSES
 
-include { salmon_quant; oarfish_dtu_quant; create_summary_snippet; terminus_collapse } from "dtu_base.nf"
+include { salmon_quant; decompress_annotation_dtu; oarfish_dtu_quant; create_summary_snippet; terminus_collapse } from "dtu_base.nf"
 
 process salmon_idx{
     conda "$COUNTENV"+".yaml"
@@ -183,7 +183,9 @@ workflow DTU{
                 element -> return "${workflow.workDir}/../MAPPED/${COMBO}/"+element+"_mapped_sorted.bam"
             }
         mapsamples_ch = Channel.fromPath(MAPPEDSAMPLES.sort())
-        oarfish_dtu_quant(mapsamples_ch.collate(1))
+        decompress_annotation_dtu(annofile)
+        annogtf_dtu = decompress_annotation_dtu.out.anno_plain
+        oarfish_dtu_quant(annogtf_dtu.combine(mapsamples_ch.collate(1)))
         quantcounts = oarfish_dtu_quant.out.counts
     }
 
diff --git a/workflows/dtu_base.nf b/workflows/dtu_base.nf
index 0948f95e..8ce085b7 100644
--- a/workflows/dtu_base.nf
+++ b/workflows/dtu_base.nf
@@ -62,6 +62,30 @@ process salmon_quant{
     }
 }
 
+process decompress_annotation_dtu{
+    conda "$COUNTENV"+".yaml"
+    container "oras://jfallmann/monsda:"+"$COUNTENV"
+    cpus 1
+	cache 'lenient'
+
+    publishDir "${workflow.workDir}/../" , mode: 'link',
+    saveAs: {filename ->
+        if (filename.indexOf("log") > 0)        "LOGS/${SCOMBO}/DTU/"+"${COUNTENV}"+"/decompress_annotation.log"
+    }
+
+    input:
+    path anno
+
+    output:
+    path "annotation.gtf", emit: anno_plain
+    path "log", emit: log
+
+    script:
+    """
+    zcat -f $anno > annotation.gtf 2> log; if [ ! -s annotation.gtf ]; then echo "ERROR: decompressed annotation from $anno is empty, check source file and filesystem" >> log; exit 1; fi
+    """
+}
+
 process oarfish_dtu_quant{
     conda "$COUNTENV"+".yaml"
     container "oras://jfallmann/monsda:"+"$COUNTENV"
@@ -75,20 +99,22 @@ process oarfish_dtu_quant{
     }
 
     input:
-    path bam
+    path fls
 
     output:
     path "*.gz", includeInputs:false, emit: counts
     path "*.log", emit: logs
 
     script:
+    anno = fls[0]
+    bam = fls[1]
     fn = file(bam).getSimpleName().replaceAll(/\Q_mapped_sorted\E/,"")
     lf = "${COUNTENV}_"+fn+".log"
     prefix = fn+"/"+COUNTENV
     oz = fn+"/quant.sf.gz"
     ol = fn+"_counts.gz"
     """
-    mkdir -p $fn; samtools collate -@ ${task.cpus} -o namecollated.bam $bam &>> $lf; zcat -f $DTUANNO > $fn/annotation.gtf 2>> $lf; $COUNTBIN --threads ${task.cpus} --genome-alignments namecollated.bam --annotation $fn/annotation.gtf --genome-fasta $DTUREF $COUNTPARAMS --output $prefix &>> $lf && rm -f namecollated.bam $fn/annotation.gtf && python3 $BINS/Analysis/oarfish_to_salmon.py -i ${prefix}.quant -o $oz &>> $lf && ln -fs $oz $ol
+    mkdir -p $fn; : > $lf; if [ ! -s $anno ]; then echo "ERROR: decompressed annotation $anno is empty, check source file and filesystem" >> $lf; exit 1; fi; samtools collate -@ ${task.cpus} -o namecollated.bam $bam &>> $lf; $COUNTBIN --threads ${task.cpus} --genome-alignments namecollated.bam --annotation $anno --genome-fasta $DTUREF $COUNTPARAMS --output $prefix &>> $lf && rm -f namecollated.bam && python3 $BINS/Analysis/oarfish_to_salmon.py -i ${prefix}.quant -o $oz &>> $lf && ln -fs $oz $ol
     """
 }
 
diff --git a/workflows/dtu_base.smk b/workflows/dtu_base.smk
index f8daf4af..61142ff2 100644
--- a/workflows/dtu_base.smk
+++ b/workflows/dtu_base.smk
@@ -73,9 +73,18 @@ else:
     # is needed, output is normalized to the salmon quant.sf schema so
     # downstream DTU tooling (tximport type="salmon", build_DTU_table.py,
     # SPIT.py) does not need to change.
+    rule decompress_annotation:
+        input:  anno = ANNOTATION
+        output: anno = temp("DTU/{combo}/"+COUNTENV+"/annotation.gtf")
+        log:    "LOGS/{combo}/DTU/"+COUNTENV+"/decompress_annotation.log"
+        conda:  ""+COUNTENV+".yaml"
+        container: "oras://jfallmann/monsda:"+COUNTENV+""
+        threads: 1
+        shell:  "zcat -f {input.anno} > {output.anno} 2> {log}; if [ ! -s {output.anno} ]; then echo 'ERROR: decompressed annotation from {input.anno} is empty, check source file and filesystem' >> {log}; exit 1; fi"
+
     rule mapping:
         input:  bam = expand("MAPPED/{scombo}/{{file}}_mapped_sorted.bam", scombo=scombo),
-                anno = ANNOTATION,
+                anno = rules.decompress_annotation.output.anno,
                 fa = REFERENCE
         output: cnts = report("DTU/{combo}/"+COUNTENV+"/{file}_counts.sf.gz", category="COUNTING"),
                 ctsdir = report(directory("DTU/{combo}/"+COUNTENV+"/{file}"), category="COUNTING")
@@ -86,11 +95,10 @@ else:
         params: cpara = lambda wildcards: tool_params(wildcards.file, None, config, 'DTU', DTUENV)['OPTIONS'].get('QUANT', ""),
                 mapp = COUNTBIN,
                 nbam = lambda wildcards, output: os.path.join(str(output.ctsdir), "namecollated.bam"),
-                anno = lambda wildcards, output: os.path.join(str(output.ctsdir), "annotation.gtf"),
                 prefix = lambda wildcards, output: os.path.join(str(output.ctsdir), COUNTENV),
                 linksf = lambda wildcards, output: str(os.path.abspath(output.ctsdir)),
                 bins = BINS
-        shell: "set +euo pipefail; mkdir -p {output.ctsdir}; samtools collate -@ {threads} -o {params.nbam} {input.bam} &>> {log}; zcat -f {input.anno} > {params.anno} 2>> {log}; {params.mapp} --threads {threads} --genome-alignments {params.nbam} --annotation {params.anno} --genome-fasta {input.fa} {params.cpara} --output {params.prefix} &>> {log} && rm -f {params.nbam} {params.anno} && python3 {params.bins}/Analysis/oarfish_to_salmon.py -i {params.prefix}.quant -o {output.ctsdir}/quant.sf.gz &>> {log} ; ln -fs {params.linksf}/quant.sf.gz {output.cnts} &>> {log}"
+        shell: "set +euo pipefail; mkdir -p {output.ctsdir}; samtools collate -@ {threads} -o {params.nbam} {input.bam} &>> {log}; {params.mapp} --threads {threads} --genome-alignments {params.nbam} --annotation {input.anno} --genome-fasta {input.fa} {params.cpara} --output {params.prefix} &>> {log} && rm -f {params.nbam} && python3 {params.bins}/Analysis/oarfish_to_salmon.py -i {params.prefix}.quant -o {output.ctsdir}/quant.sf.gz &>> {log} ; ln -fs {params.linksf}/quant.sf.gz {output.cnts} &>> {log}"
 
 
 if runterminus:
diff --git a/workflows/edger_DE.nf b/workflows/edger_DE.nf
index 9b8f4b37..5966e26b 100644
--- a/workflows/edger_DE.nf
+++ b/workflows/edger_DE.nf
@@ -24,6 +24,30 @@ COUNTENV = (COUNTTOOL == 'featureCounts') ? 'countreads_de' : COUNTTOOL
 
 //DE PROCESSES
 
+process decompress_annotation_edger{
+    conda "$COUNTENV"+".yaml"
+    container "oras://jfallmann/monsda:"+"$COUNTENV"
+    cpus 1
+	cache 'lenient'
+
+    publishDir "${workflow.workDir}/../" , mode: 'link',
+    saveAs: {filename ->
+        if (filename.indexOf("log") > 0)        "LOGS/${SCOMBO}/DE/edger/decompress_annotation.log"
+    }
+
+    input:
+    path anno
+
+    output:
+    path "annotation.gtf", emit: anno_plain
+    path "log", emit: log
+
+    script:
+    """
+    zcat -f $anno > annotation.gtf 2> log; if [ ! -s annotation.gtf ]; then echo "ERROR: decompressed annotation from $anno is empty, check source file and filesystem" >> log; exit 1; fi
+    """
+}
+
 process featurecount_edger{
     conda "$COUNTENV"+".yaml"
     container "oras://jfallmann/monsda:"+"$COUNTENV"
@@ -69,7 +93,7 @@ process featurecount_edger{
             stranded = ''
     }
     """
-    mkdir -p TMP; zcat -f $anno > annotation.gtf 2> $ol; $COUNTBIN -T ${task.cpus} $COUNTPARAMS $pair $stranded -a annotation.gtf -o tmpcts $reads 2>> $ol && rm -f annotation.gtf && head -n2 tmpcts |gzip > $oc && export LC_ALL=C; tail -n+3 tmpcts|sort --parallel=${task.cpus} -S $sortmem -T TMP -k1,1 -k2,2n -k3,3n -u |gzip >> $oc 2>> $ol && mv tmpcts.summary $os
+    mkdir -p TMP; : > $ol; if [ ! -s $anno ]; then echo "ERROR: decompressed annotation $anno is empty, check source file and filesystem" >> $ol; exit 1; fi; $COUNTBIN -T ${task.cpus} $COUNTPARAMS $pair $stranded -a $anno -o tmpcts $reads 2>> $ol && head -n2 tmpcts |gzip > $oc && export LC_ALL=C; tail -n+3 tmpcts|sort --parallel=${task.cpus} -S $sortmem -T TMP -k1,1 -k2,2n -k3,3n -u |gzip >> $oc 2>> $ol && mv tmpcts.summary $os
     """
 }
 
@@ -103,7 +127,7 @@ process oarfish_gene_count{
     os = fn+".counts.summary"
     ol = fn+".log"
     """
-    samtools collate -@ ${task.cpus} -o namecollated.bam $bam &>> $ol; zcat -f $anno > annotation.gtf 2>> $ol; $COUNTBIN --threads ${task.cpus} --genome-alignments namecollated.bam --annotation annotation.gtf --genome-fasta $DEREF $QUANTPARAMS --output $fn &>> $ol && rm -f namecollated.bam annotation.gtf && python3 $BINS/Analysis/oarfish_to_featurecounts.py -i ${fn}.quant -g $anno -s ${fn}_mapped_sorted.bam -o $oc 2>> $ol && touch $os
+    : > $ol; if [ ! -s $anno ]; then echo "ERROR: decompressed annotation $anno is empty, check source file and filesystem" >> $ol; exit 1; fi; samtools collate -@ ${task.cpus} -o namecollated.bam $bam &>> $ol; $COUNTBIN --threads ${task.cpus} --genome-alignments namecollated.bam --annotation $anno --genome-fasta $DEREF $QUANTPARAMS --output $fn &>> $ol && rm -f namecollated.bam && python3 $BINS/Analysis/oarfish_to_featurecounts.py -i ${fn}.quant -g $anno -s ${fn}_mapped_sorted.bam -o $oc 2>> $ol && touch $os
     """
 }
 
@@ -283,6 +307,9 @@ workflow DE{
     annofile = Channel.fromPath(DEANNO)
     //annofile.subscribe {  println "ANNO: $it \t COMBO: ${COMBO} SCOMBO: ${SCOMBO} LONG: ${LONGSAMPLES}"  }
 
+    decompress_annotation_edger(annofile)
+    annogtf = decompress_annotation_edger.out.anno_plain
+
     if (COUNTTOOL == 'featureCounts'){
         if (RUNDEDUP){
             MAPPEDSAMPLES = LONGSAMPLES.collect{
@@ -297,7 +324,7 @@ workflow DE{
         mapsamples_ch = Channel.fromPath(MAPPEDSAMPLES.sort())
         //mapsamples_ch.subscribe {  println "MAP: $it \t COMBO: ${COMBO} SCOMBO: ${SCOMBO} LONG: ${LONGSAMPLES}"  }
 
-        featurecount_edger(annofile.combine(mapsamples_ch.collate(1)))
+        featurecount_edger(annogtf.combine(mapsamples_ch.collate(1)))
         countcts = featurecount_edger.out.fc_cts
     }else{
         MAPPEDSAMPLES = LONGSAMPLES.collect{
@@ -305,7 +332,7 @@ workflow DE{
         }
         mapsamples_ch = Channel.fromPath(MAPPEDSAMPLES.sort())
 
-        oarfish_gene_count(annofile.combine(mapsamples_ch.collate(1)))
+        oarfish_gene_count(annogtf.combine(mapsamples_ch.collate(1)))
         countcts = oarfish_gene_count.out.fc_cts
     }
 
diff --git a/workflows/edger_DE.smk b/workflows/edger_DE.smk
index 94c02d26..5fdcda3f 100644
--- a/workflows/edger_DE.smk
+++ b/workflows/edger_DE.smk
@@ -29,9 +29,19 @@ rule themall:
             Rmd     = expand("REPORTS/SUMMARY/RmdSnippets/{combo}.Rmd", combo=combo),
             postde = expand("POSTDE/{combo}", combo=combo) if postde_enabled else []
 
+rule decompress_annotation:
+    input:  anno = ANNOTATION
+    output: anno = temp("DE/{combo}/Featurecounts/annotation.gtf")
+    log:    "LOGS/{combo}/DE/edger/decompress_annotation.log"
+    conda:  ""+COUNTENV+".yaml"
+    container: "oras://jfallmann/monsda:"+COUNTENV+""
+    threads: 1
+    shell:  "zcat -f {input.anno} > {output.anno} 2> {log}; if [ ! -s {output.anno} ]; then echo 'ERROR: decompressed annotation from {input.anno} is empty, check source file and filesystem' >> {log}; exit 1; fi"
+
 if COUNTTOOL == 'featureCounts':
     rule featurecount_unique:
-        input:  reads = expand("MAPPED/{scombo}/{{file}}_mapped_sorted_unique.bam", scombo=scombo) if not usededup else expand("MAPPED/{scombo}/{{file}}_mapped_sorted_unique_dedup.bam", scombo=scombo)
+        input:  reads = expand("MAPPED/{scombo}/{{file}}_mapped_sorted_unique.bam", scombo=scombo) if not usededup else expand("MAPPED/{scombo}/{{file}}_mapped_sorted_unique_dedup.bam", scombo=scombo),
+                anno  = rules.decompress_annotation.output.anno
         output: tmp   = temp("DE/{combo}/Featurecounts/{file}_tmp.counts"),
                 tmph  = temp("DE/{combo}/Featurecounts/{file}_tmp.head.gz"),
                 tmpc  = temp("DE/{combo}/Featurecounts/{file}_tmp.count.gz"),
@@ -41,30 +51,30 @@ if COUNTTOOL == 'featureCounts':
         container: "oras://jfallmann/monsda:"+COUNTENV+""
         threads: MAXTHREAD
         params: countb = COUNTBIN,
-                anno = ANNOTATION,
                 cpara = lambda wildcards: tool_params(wildcards.file, None, config, "DE", DEENV.split('_')[0])['OPTIONS'].get('COUNT', ""),
                 paired   = lambda x: '-p' if paired == 'paired' else '',
                 stranded = lambda x: '-s 1' if stranded == 'fr' else '-s 2' if stranded == 'rf' else '',
                 sortmem = get_sortmem,
                 prefix = lambda wildcards: "DE/"+combo+"/Featurecounts/"+wildcards.file
-        shell:  "mkdir -p $(dirname {params.prefix}); zcat -f {params.anno} > {params.prefix}_annotation.gtf 2> {log}; {params.countb} -T {threads} {params.cpara} {params.paired} {params.stranded} -a {params.prefix}_annotation.gtf -o {output.tmp} {input.reads} 2>> {log} && rm -f {params.prefix}_annotation.gtf && head -n2 {output.tmp} |gzip > {output.tmph} && export LC_ALL=C; tail -n+3 {output.tmp}|sort --parallel={threads} -S {params.sortmem}G -T TMP -k1,1 -k2,2n -k3,3n -u |gzip >> {output.tmpc} && zcat {output.tmph} {output.tmpc} |gzip > {output.cts} && mv {output.tmp}.summary {output.cts}.summary"
+        shell:  "mkdir -p $(dirname {params.prefix}); {params.countb} -T {threads} {params.cpara} {params.paired} {params.stranded} -a {input.anno} -o {output.tmp} {input.reads} 2> {log} && head -n2 {output.tmp} |gzip > {output.tmph} && export LC_ALL=C; tail -n+3 {output.tmp}|sort --parallel={threads} -S {params.sortmem}G -T TMP -k1,1 -k2,2n -k3,3n -u |gzip >> {output.tmpc} && zcat {output.tmph} {output.tmpc} |gzip > {output.cts} && mv {output.tmp}.summary {output.cts}.summary"
 else:
     # Long-read quantifiers (e.g. oarfish) quantify directly from the
     # genome-mapped BAM and are aggregated to gene level afterwards.
     rule featurecount_unique:
-        input:  reads = expand("MAPPED/{scombo}/{{file}}_mapped_sorted.bam", scombo=scombo)
+        input:  reads = expand("MAPPED/{scombo}/{{file}}_mapped_sorted.bam", scombo=scombo),
+                anno  = rules.decompress_annotation.output.anno
         output: cts   = "DE/{combo}/Featurecounts/{file}_mapped_sorted_unique.counts.gz" if not usededup else "DE/{combo}/Featurecounts/{file}_mapped_sorted_unique_dedup.counts.gz"
         log:    "LOGS/{combo}/{file}/DE/edger/"+COUNTENV+"_edger_unique.log"
         conda:  ""+COUNTENV+".yaml"
         container: "oras://jfallmann/monsda:"+COUNTENV+""
         threads: MAXTHREAD
         params: countb = COUNTBIN,
-                anno = ANNOTATION,
+                origanno = ANNOTATION,
                 ref = REFERENCE,
                 cpara = lambda wildcards: tool_params(wildcards.file, None, config, "DE", DEENV.split('_')[0])['OPTIONS'].get('QUANT', ""),
                 bins = BINS,
                 prefix = lambda wildcards: "DE/"+combo+"/Featurecounts/"+wildcards.file
-        shell:  "mkdir -p $(dirname {params.prefix}); samtools collate -@ {threads} -o {params.prefix}_namecollated.bam {input.reads} 2> {log}; zcat -f {params.anno} > {params.prefix}_annotation.gtf 2>> {log}; {params.countb} --threads {threads} --genome-alignments {params.prefix}_namecollated.bam --annotation {params.prefix}_annotation.gtf --genome-fasta {params.ref} {params.cpara} --output {params.prefix} 2>> {log} && rm -f {params.prefix}_namecollated.bam {params.prefix}_annotation.gtf && python3 {params.bins}/Analysis/oarfish_to_featurecounts.py -i {params.prefix}.quant -g {params.anno} -s {wildcards.file}_mapped_sorted.bam -o {output.cts} 2>> {log}"
+        shell:  "mkdir -p $(dirname {params.prefix}); samtools collate -@ {threads} -o {params.prefix}_namecollated.bam {input.reads} 2> {log}; {params.countb} --threads {threads} --genome-alignments {params.prefix}_namecollated.bam --annotation {input.anno} --genome-fasta {params.ref} {params.cpara} --output {params.prefix} 2>> {log} && rm -f {params.prefix}_namecollated.bam && python3 {params.bins}/Analysis/oarfish_to_featurecounts.py -i {params.prefix}.quant -g {params.origanno} -s {wildcards.file}_mapped_sorted.bam -o {output.cts} 2>> {log}"
 
 rule prepare_count_table:
     input:   cnd  = expand(rules.featurecount_unique.output.cts, combo=combo, file=samplecond(SAMPLES, config))
diff --git a/workflows/header.smk b/workflows/header.smk
index 29496a2b..3fec00b6 100644
--- a/workflows/header.smk
+++ b/workflows/header.smk
@@ -326,6 +326,11 @@ if 'FUSIONS' in config:
         ANNOTATION = ANNO.get('GTF') if 'GTF' in ANNO and ANNO.get('GTF') != '' else ANNO.get('GFF')  # by default GTF format will be used
 
 
+if ANNOTATION and isinstance(ANNOTATION, str):
+    # Resolve once to an absolute path so every rule's shell command can read
+    # it reliably regardless of its own working directory (e.g. containers).
+    ANNOTATION = os.path.abspath(ANNOTATION)
+
 combo = ''
 
 if ANNOTATION:
diff --git a/workflows/oarfish.nf b/workflows/oarfish.nf
index 05857a35..0fb889c9 100644
--- a/workflows/oarfish.nf
+++ b/workflows/oarfish.nf
@@ -10,6 +10,30 @@ COUNTPARAMS = get_always('oarfish_params_COUNT') ?: ''
 
 //COUNTING PROCESSES
 
+process decompress_annotation_oarfish{
+    conda "$COUNTENV"+".yaml"
+    container "oras://jfallmann/monsda:"+"$COUNTENV"
+    cpus 1
+	cache 'lenient'
+
+    publishDir "${workflow.workDir}/../" , mode: 'link',
+    saveAs: {filename ->
+        if (filename.indexOf("log") > 0)        "LOGS/${COMBO}/COUNTING/oarfish/decompress_annotation.log"
+    }
+
+    input:
+    path anno
+
+    output:
+    path "annotation.gtf", emit: anno_plain
+    path "log", emit: log
+
+    script:
+    """
+    zcat -f $anno > annotation.gtf 2> log; if [ ! -s annotation.gtf ]; then echo "ERROR: decompressed annotation from $anno is empty, check source file and filesystem" >> log; exit 1; fi
+    """
+}
+
 process oarfish_quant{
     conda "$COUNTENV"+".yaml"
     container "oras://jfallmann/monsda:"+"$COUNTENV"
@@ -23,7 +47,7 @@ process oarfish_quant{
     }
 
     input:
-    path bam
+    path fls
 
     output:
     path "*.gz", includeInputs:false, emit: counts
@@ -31,12 +55,14 @@ process oarfish_quant{
     path "*", includeInputs:false, emit: rest
 
     script:
+    anno = fls[0]
+    bam = fls[1]
     fn = file(bam).getSimpleName().replaceAll(/\Q_mapped_sorted\E/,"")
     lf = "oarfish_"+fn+".log"
     oz = fn+"/quant.sf.gz"
     ol = fn+"_counts.gz"
     """
-    mkdir -p $fn; samtools collate -@ ${task.cpus} -o namecollated.bam $bam &>> $lf; zcat -f $COUNTANNO > $fn/annotation.gtf 2>> $lf; $COUNTBIN --threads ${task.cpus} --genome-alignments namecollated.bam --annotation $fn/annotation.gtf --genome-fasta $COUNTREF $COUNTPARAMS --output $fn/oarfish &>> $lf && rm -f namecollated.bam $fn/annotation.gtf && python3 $BINS/Analysis/oarfish_to_salmon.py -i $fn/oarfish.quant -o $oz &>> $lf && ln -fs $oz $ol
+    mkdir -p $fn; : > $lf; if [ ! -s $anno ]; then echo "ERROR: decompressed annotation $anno is empty, check source file and filesystem" >> $lf; exit 1; fi; samtools collate -@ ${task.cpus} -o namecollated.bam $bam &>> $lf; $COUNTBIN --threads ${task.cpus} --genome-alignments namecollated.bam --annotation $anno --genome-fasta $COUNTREF $COUNTPARAMS --output $fn/oarfish &>> $lf && rm -f namecollated.bam && python3 $BINS/Analysis/oarfish_to_salmon.py -i $fn/oarfish.quant -o $oz &>> $lf && ln -fs $oz $ol
     """
 }
 
@@ -50,8 +76,11 @@ workflow COUNTING{
     }
 
     mapsamples_ch = Channel.fromPath(MAPPEDSAMPLES.sort())
+    annofile = Channel.fromPath(COUNTANNO)
+    decompress_annotation_oarfish(annofile)
+    annogtf = decompress_annotation_oarfish.out.anno_plain
 
-    oarfish_quant(mapsamples_ch.collate(1))
+    oarfish_quant(annogtf.combine(mapsamples_ch.collate(1)))
 
     emit:
     counts = oarfish_quant.out.counts
diff --git a/workflows/oarfish.smk b/workflows/oarfish.smk
index 52396b44..d7818bb6 100644
--- a/workflows/oarfish.smk
+++ b/workflows/oarfish.smk
@@ -8,9 +8,18 @@ unik = get_dict_hash(keydict)
 rule themall:
     input:  expand("COUNTS/{combo}/{file}_counts.sf.gz", combo=combo, file=samplecond(SAMPLES, config))
 
+rule decompress_annotation:
+    input:  anno = ANNOTATION
+    output: anno = temp("COUNTS/{combo}/annotation.gtf")
+    log:    "LOGS/{combo}/COUNTING/oarfish/decompress_annotation.log"
+    conda:  ""+COUNTENV+".yaml"
+    container: "oras://jfallmann/monsda:"+COUNTENV+""
+    threads: 1
+    shell:  "zcat -f {input.anno} > {output.anno} 2> {log}; if [ ! -s {output.anno} ]; then echo 'ERROR: decompressed annotation from {input.anno} is empty, check source file and filesystem' >> {log}; exit 1; fi"
+
 rule mapping:
     input:  bam = expand("MAPPED/{scombo}/{{file}}_mapped_sorted.bam", scombo=scombo),
-            anno = ANNOTATION,
+            anno = rules.decompress_annotation.output.anno,
             fa = REFERENCE
     output: cnts = report("COUNTS/{combo}/{file}_counts.sf.gz", category="COUNTING"),
             ctsdir = report(directory("COUNTS/{combo}/{file}"), category="COUNTING")
@@ -21,8 +30,7 @@ rule mapping:
     params: cpara = lambda wildcards: tool_params(wildcards.file, None, config, 'COUNTING', COUNTENV)['OPTIONS'].get('COUNT', ""),
             mapp = COUNTBIN,
             nbam = lambda wildcards, output: os.path.join(str(output.ctsdir), "namecollated.bam"),
-            anno = lambda wildcards, output: os.path.join(str(output.ctsdir), "annotation.gtf"),
             prefix = lambda wildcards, output: os.path.join(str(output.ctsdir), "oarfish"),
             linksf = lambda wildcards, output: str(os.path.abspath(output.ctsdir)),
             bins = BINS
-    shell: "set +euo pipefail; mkdir -p {output.ctsdir}; samtools collate -@ {threads} -o {params.nbam} {input.bam} &>> {log}; zcat -f {input.anno} > {params.anno} 2>> {log}; {params.mapp} --threads {threads} --genome-alignments {params.nbam} --annotation {params.anno} --genome-fasta {input.fa} {params.cpara} --output {params.prefix} &>> {log} && rm -f {params.nbam} {params.anno} && python3 {params.bins}/Analysis/oarfish_to_salmon.py -i {params.prefix}.quant -o {output.ctsdir}/quant.sf.gz &>> {log} ; ln -fs {params.linksf}/quant.sf.gz {output.cnts} &>> {log}"
+    shell: "set +euo pipefail; mkdir -p {output.ctsdir}; samtools collate -@ {threads} -o {params.nbam} {input.bam} &>> {log}; {params.mapp} --threads {threads} --genome-alignments {params.nbam} --annotation {input.anno} --genome-fasta {input.fa} {params.cpara} --output {params.prefix} &>> {log} && rm -f {params.nbam} && python3 {params.bins}/Analysis/oarfish_to_salmon.py -i {params.prefix}.quant -o {output.ctsdir}/quant.sf.gz &>> {log} ; ln -fs {params.linksf}/quant.sf.gz {output.cnts} &>> {log}"
diff --git a/workflows/spit_DTU.nf b/workflows/spit_DTU.nf
index 4800f025..2ae920e5 100644
--- a/workflows/spit_DTU.nf
+++ b/workflows/spit_DTU.nf
@@ -27,7 +27,7 @@ PCOMBO = get_always('COMBO') ?: 'none'
 
 //DTU PROCESSES
 
-include { salmon_quant; oarfish_dtu_quant; create_summary_snippet; terminus_collapse } from "dtu_base.nf"
+include { salmon_quant; decompress_annotation_dtu; oarfish_dtu_quant; create_summary_snippet; terminus_collapse } from "dtu_base.nf"
 
 process salmon_idx{
     conda "$COUNTENV"+".yaml"
@@ -181,7 +181,9 @@ workflow DTU{
                 element -> return "${workflow.workDir}/../MAPPED/${COMBO}/"+element+"_mapped_sorted.bam"
             }
         mapsamples_ch = Channel.fromPath(MAPPEDSAMPLES.sort())
-        oarfish_dtu_quant(mapsamples_ch.collate(1))
+        decompress_annotation_dtu(annofile)
+        annogtf_dtu = decompress_annotation_dtu.out.anno_plain
+        oarfish_dtu_quant(annogtf_dtu.combine(mapsamples_ch.collate(1)))
         quantcounts = oarfish_dtu_quant.out.counts
     }