New container images

Makefile

@@ -1,16 +1,19 @@
 docker-imgs:
-	docker build --platform linux/amd64 -t medbioinf/ident-comparison-python:latest -f docker/python/Dockerfile .
+	docker pull ghcr.io/medbioinf/pipeline-of-identification:latest
 
 	docker pull proteowizard/pwiz-skyline-i-agree-to-the-vendor-licenses:3.0.25073-842baef
-
-	docker pull quay.io/medbioinf/openms:3.1.0
+	docker pull quay.io/medbioinf/tdf2mzml:0.4
+	docker pull quay.io/medbioinf/openms:3.4.1
+	docker pull quay.io/medbioinf/fdrbench-nightly:146f77
 
 	docker pull quay.io/medbioinf/comet-ms:v2024.01.0
-	docker pull quay.io/medbioinf/sage:v0.14.7
-	docker pull quay.io/medbioinf/xtandem:2017.2.1.4
+	docker pull quay.io/medbioinf/maxquant:2.6.3.0
 	docker pull quay.io/medbioinf/msamanda:3.0.22.071
 	docker pull quay.io/medbioinf/msgfplus:v2024.03.26
-
 	docker pull quay.io/medbioinf/mzid-merger:1.4.26
+	docker pull quay.io/medbioinf/sage:v0.15.0-beta.1
+	docker pull quay.io/medbioinf/xtandem:2017.2.1.4
+
+	docker pull ghcr.io/percolator/percolator:branch-3-08
 
-	docker pull quay.io/medbioinf/percolator:3.6.5
+	docker build --platform linux/amd64 -t medbioinf/msfragger -f docker/msfragger/Dockerfile docker/msfragger/.

docker/msfragger/Dockerfile

@@ -1,9 +1,8 @@
-FROM --platform=amd64 mambaorg/micromamba:2.1.1-ubuntu22.04
+FROM mambaorg/micromamba:2.3.1-ubuntu24.04
 
-WORKDIR /home/mambauser
 # Copy environment.yml and requirements.txt
-COPY --chown=mambauser:mambauser environment.yml .
-COPY --chown=mambauser:mambauser requirements.txt .
+COPY --chown=mambauser:mambauser environment.yml /home/mambauser/
+COPY --chown=mambauser:mambauser requirements.txt /home/mambauser/
 
 # copy over MSFragger bin
 COPY --chown=mambauser:mambauser ./MSFragger-4.2.zip /tmp/
@@ -12,10 +11,10 @@ COPY --chown=mambauser:mambauser ./MSFragger-4.2.zip /tmp/
 USER mambauser
 ENV HOME=/home/mambauser
 ENV ENV_NAME=medbioinforub-msfragger
+WORKDIR /home/mambauser
 
-RUN echo 'show_banner: false' > ~/.mambarc
-
-RUN micromamba env create -y -f environment.yml \
+RUN echo 'show_banner: false' > ~/.mambarc \
+    && micromamba env create -y -f /home/mambauser/environment.yml \
     && micromamba clean --all --yes
 
 # install / unzip MSFragger

docker/msfragger/environment.yml

@@ -9,6 +9,6 @@ dependencies:
   - setuptools
   - git
   - openjdk=21
-  - unzip=6.0
+  - conda-forge::unzip=6.0
   - pip:
     - -r requirements.txt

main.nf

@@ -3,7 +3,7 @@ nextflow.enable.dsl=2
 nextflow.preview.output = true
 
 // default python image
-params.python_image = 'medbioinf/ident-comparison-python'
+params.python_image = 'ghcr.io/medbioinf/pipeline-of-identification:latest'
 
 // parameters set by the command line
 params.raw_files = ''

src/identification/maxquant_identification.nf

@@ -1,6 +1,6 @@
 nextflow.enable.dsl=2
 
-params.maxquant_image = 'medbioinf/maxquant:v2.6.1.0'
+params.maxquant_image = 'quay.io/medbioinf/maxquant:2.6.3.0'
 
 // number of threads used by maxquant
 params.maxquant_threads = 4

src/postprocessing/percolator.nf

@@ -1,6 +1,6 @@
 nextflow.enable.dsl=2
 
-params.percolator_image = 'quay.io/medbioinf/percolator:3.6.5'
+params.percolator_image = 'ghcr.io/percolator/percolator:branch-3-08'
 
 // number of threads used by percolator
 params.percolator_threads = 4

src/preprocess/convert_to_mzml.nf

@@ -1,15 +1,17 @@
 nextflow.enable.dsl=2
 
 params.msconvert_image = 'proteowizard/pwiz-skyline-i-agree-to-the-vendor-licenses:3.0.25073-842baef'
-
+params.tdf2mzml_image = 'quay.io/medbioinf/tdf2mzml:0.4'
+params.tdf2mzml_threads = 8
 
 workflow convert_to_mzml {
     take:
     input_path
 
     main:
     if (params.is_timstof) {
-        mzml = convert_bruker_d(input_path)
+        mzml_direct_convert = convert_bruker_d(input_path)
+        mzml = adjust_mzML(mzml_direct_convert)
     } else {
         mzml = convert_thermo_raw(input_path)
     }
@@ -23,6 +25,7 @@ workflow convert_to_mzml {
 
 process convert_thermo_raw {
     cpus 2
+    memory "8 GB"
     container { params.msconvert_image }
 
     input:
@@ -38,24 +41,51 @@ process convert_thermo_raw {
 }
 
 process convert_bruker_d {
-    cpus 2
-    container { params.python_image }
+    cpus { params.tdf2mzml_threads }
+    memory "8 GB"
+    container { params.tdf2mzml_image }
 
     input:
-    path input_raw
+    path input_d
 
     output:
-    path "${input_raw.baseName}.mzML"
+    path "${input_d.baseName}.mzML"
 
     script:
     """
-    # here goes the converter...
+    export MKL_NUM_THREADS=${params.tdf2mzml_threads}
+    export NUMEXPR_NUM_THREADS=${params.tdf2mzml_threads}
+    export OMP_NUM_THREADS=${params.tdf2mzml_threads}
 
+    tdf2mzml -i ${input_d} --compression "zlib" -o ${input_d.baseName}.mzML
+    """
+}
+
+process adjust_mzML {
+    cpus 2
+    memory "8 GB"
+    container { params.msconvert_image }
+
+    input:
+    path input_mzML
+
+    output:
+    path "uncompressed/${input_mzML.baseName}.mzML"
+
+    script:
+    """
     # msamanda needs explicit "scan=" in the id of a scan (not there in e.g. TimsTOF converted mzML data)
-    sed -i -e 's/<spectrum\\(.*\\) id="index=\\([0-9]*\\)\\(.*\\)/<spectrum\\1 id="index=\\2 scan=\\2\\3/;s/spectrumRef="\\(.*\\)index=\\([0-9]*\\)\\(.*\\)"/spectrumRef="\\1index=\\2 scan=\\2\\3"/' ${input_raw.baseName}.mzML
+    sed -e 's/<spectrum\\(.*\\) id="index=\\([0-9]*\\)\\(.*\\)/<spectrum\\1 id="index=\\2 scan=\\2\\3/;s/spectrumRef="\\(.*\\)index=\\([0-9]*\\)\\(.*\\)"/spectrumRef="\\1index=\\2 scan=\\2\\3"/' ${input_mzML} > ${input_mzML.baseName}.reindex.mzML
 
     # after this, the mzML index needs to be removed, or just the compression???
-    ## docker run --rm -it -v ./:/data/ proteowizard/pwiz-skyline-i-agree-to-the-vendor-licenses:3.0.25073-842baef wine msconvert --mzML -o /data/rem-index --noindex --zlib=off /data/${file};
+    ## docker run --rm -it -v ./:/data/ proteowizard/pwiz-skyline-i-agree-to-the-vendor-licenses:3.0.25073-842baef wine msconvert --mzML -o ${input_mzML}.noindex_nocompress.mzML --noindex --zlib=off ${input_mzML};
+
+    # uncompress the mzML with re-named id-tags (this re-calculates also the index, but for X!Tandem it is needed uncompressed anyways)
+    mkdir uncompressed
+    wine msconvert --mzML --zlib=off -o uncompressed --outfile ${input_mzML.baseName}.mzML ${input_mzML.baseName}.reindex.mzML
+
+    # cleanup
+    rm ${input_mzML.baseName}.reindex.mzML
     """
 }
 

src/preprocess/create_decoy_database.nf

@@ -1,6 +1,6 @@
 nextflow.enable.dsl=2
 
-params.openms_image = 'quay.io/medbioinf/openms:3.1.0'
+params.openms_image = 'quay.io/medbioinf/openms:3.4.1'
 
 // number of threads used by maxquant
 params.decoy_database_threads = 4