Merge pull request #28 from bigbio/dev

u
bigbio · Dec 7, 2022 · 51e568b · 51e568b
2 parents e42d879 + f563e4d
commit 51e568b
Show file tree

Hide file tree

Showing 9 changed files with 22 additions and 21 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -61,7 +61,7 @@ The pipeline is using Nextflow DSL2, each process will be run with its own [Bioc
 | `comet`               | 2021010    |
 | `msgf+`               | 2022.01.07 |
 | `openms`              | 2.8.0      |
-| `sdrf-pipelines`      | 0.0.21     |
+| `sdrf-pipelines`      | 0.0.22     |
 | `percolator`          | 3.5        |
 | `pmultiqc`            | 0.0.11     |
 | `luciphor`            | 2020_04_03 |

diff --git a/bin/diann_convert.py b/bin/diann_convert.py
@@ -174,7 +174,7 @@ def convert(ctx, folder, dia_params, diann_version, charge, missed_cleavages, qv
         MTD.loc["", :] = ""
         PRH.loc[len(PRH) + 1, :] = ""
         PEH.loc[len(PEH) + 1, :] = ""
-        with open(os.path.splitext(os.path.basename(exp_design))[0] + "_out.mztab", "w", newline="") as f:
+        with open(os.path.splitext(os.path.basename(exp_design))[0] + "_out.mzTab", "w", newline="") as f:
             MTD.to_csv(f, mode="w", sep="\t", index=False, header=False)
             PRH.to_csv(f, mode="w", sep="\t", index=False, header=True)
             PEH.to_csv(f, mode="w", sep="\t", index=False, header=True)

diff --git a/modules/local/diannconvert/main.nf b/modules/local/diannconvert/main.nf
@@ -2,11 +2,11 @@ process DIANNCONVERT {
     tag "$meta.experiment_id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "conda-forge::pandas_schema conda-forge::lzstring bioconda::pmultiqc=0.0.17" : null)
+    conda (params.enable_conda ? "conda-forge::pandas_schema conda-forge::lzstring bioconda::pmultiqc=0.0.19" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/pmultiqc:0.0.17--pyhdfd78af_0"
+        container "https://depot.galaxyproject.org/singularity/pmultiqc:0.0.19--pyhdfd78af_0"
     } else {
-        container "quay.io/biocontainers/pmultiqc:0.0.17--pyhdfd78af_0"
+        container "quay.io/biocontainers/pmultiqc:0.0.19--pyhdfd78af_0"
     }
 
     input:
@@ -22,7 +22,7 @@ process DIANNCONVERT {
     output:
     path "*msstats_in.csv", emit: out_msstats
     path "*triqler_in.tsv", emit: out_triqler
-    path "*.mztab", emit: out_mztab
+    path "*.mzTab", emit: out_mztab
     path "versions.yml", emit: version
 
     exec:

diff --git a/modules/local/generate_diann_cfg/main.nf b/modules/local/generate_diann_cfg/main.nf
@@ -2,11 +2,11 @@ process GENERATE_DIANN_CFG {
     tag "$meta.experiment_id"
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::pandas_schema bioconda::sdrf-pipelines=0.0.21" : null)
+    conda (params.enable_conda ? "conda-forge::pandas_schema bioconda::sdrf-pipelines=0.0.22" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.21--pyhdfd78af_0"
+        container "https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.22--pyhdfd78af_0"
     } else {
-        container "quay.io/biocontainers/sdrf-pipelines:0.0.21--pyhdfd78af_0"
+        container "quay.io/biocontainers/sdrf-pipelines:0.0.22--pyhdfd78af_0"
     }
 
     input:

diff --git a/modules/local/openms/thirdparty/searchenginemsgf/main.nf b/modules/local/openms/thirdparty/searchenginemsgf/main.nf
@@ -74,6 +74,7 @@ process SEARCHENGINEMSGF {
         -max_precursor_charge $params.max_precursor_charge \\
         -min_peptide_length $params.min_peptide_length \\
         -max_peptide_length $params.max_peptide_length \\
+        -max_missed_cleavages $params.allowed_missed_cleavages \\
         -isotope_error_range $params.isotope_error_range \\
         -enzyme "${enzyme}" \\
         -tryptic ${msgf_num_enzyme_termini} \\

diff --git a/modules/local/pmultiqc/main.nf b/modules/local/pmultiqc/main.nf
@@ -1,11 +1,11 @@
 process PMULTIQC {
     label 'process_high'
 
-    conda (params.enable_conda ? "conda-forge::pandas_schema conda-forge::lzstring bioconda::pmultiqc=0.0.17" : null)
+    conda (params.enable_conda ? "conda-forge::pandas_schema conda-forge::lzstring bioconda::pmultiqc=0.0.19" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/pmultiqc:0.0.17--pyhdfd78af_0"
+        container "https://depot.galaxyproject.org/singularity/pmultiqc:0.0.19--pyhdfd78af_0"
     } else {
-        container "quay.io/biocontainers/pmultiqc:0.0.17--pyhdfd78af_0"
+        container "quay.io/biocontainers/pmultiqc:0.0.19--pyhdfd78af_0"
     }
 
     input:

diff --git a/modules/local/preprocess_expdesign.nf b/modules/local/preprocess_expdesign.nf
@@ -4,7 +4,7 @@
 // accept different file endings already?
 process PREPROCESS_EXPDESIGN {
 
-    conda (params.enable_conda ? "bioconda::sdrf-pipelines=0.0.21 conda-forge::pandas" : null)
+    conda (params.enable_conda ? "bioconda::sdrf-pipelines=0.0.22 conda-forge::pandas" : null)
 
     label 'process_very_low'
     label 'process_single_thread'

diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
@@ -1,10 +1,10 @@
 process SAMPLESHEET_CHECK {
 
-    conda (params.enable_conda ? "bioconda::sdrf-pipelines=0.0.21" : null)
+    conda (params.enable_conda ? "bioconda::sdrf-pipelines=0.0.22" : null)
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.21--pyhdfd78af_0' :
-        'quay.io/biocontainers/sdrf-pipelines:0.0.21--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.22--pyhdfd78af_0' :
+        'quay.io/biocontainers/sdrf-pipelines:0.0.22--pyhdfd78af_0' }"
 
     input:
     path input_file
@@ -24,7 +24,7 @@ process SAMPLESHEET_CHECK {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        sdrf-pipelines: \$(echo "0.0.21")
+        sdrf-pipelines: \$(echo "0.0.22")
     END_VERSIONS
     """
 }
diff --git a/modules/local/sdrfparsing/main.nf b/modules/local/sdrfparsing/main.nf
@@ -2,10 +2,10 @@ process SDRFPARSING {
     tag "$sdrf.Name"
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::pandas_schema bioconda::sdrf-pipelines=0.0.21" : null)
+    conda (params.enable_conda ? "conda-forge::pandas_schema bioconda::sdrf-pipelines=0.0.22" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.21--pyhdfd78af_0' :
-        'quay.io/biocontainers/sdrf-pipelines:0.0.21--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.22--pyhdfd78af_0' :
+        'quay.io/biocontainers/sdrf-pipelines:0.0.22--pyhdfd78af_0' }"
 
     input:
     path sdrf
@@ -31,7 +31,7 @@ process SDRFPARSING {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        sdrf-pipelines: \$(echo "0.0.21")
+        sdrf-pipelines: \$(echo "0.0.22")
     END_VERSIONS
     """
 }