jfallmann · Oct 20, 2026 · Oct 20, 2026 · Oct 20, 2026 · Oct 20, 2026 · Oct 20, 2026
diff --git a/MONSDA/Versions.py b/MONSDA/Versions.py
@@ -359,21 +359,33 @@ 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(
                 v=monsda_version,
                 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
@@ -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
@@ -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/...s/golden/config_DTU/nf/allconditions_fastqc-trimgalore-picard-star_DTU_drimseq_subflow.nf b/...s/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
@@ -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/...golden/config_DTU/smk/allconditions_fastqc-trimgalore-picard-star_DTU_dexseq_subsnake.smk b/...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/...olden/config_DTU/smk/allconditions_fastqc-trimgalore-picard-star_DTU_drimseq_subsnake.smk b/...olden/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