get software versions

.github/workflows/main-build.yml

@@ -72,21 +72,21 @@ jobs:
         parallel: true
         query: ^workflows
 
-    - name: Build nextflow schemas
-      uses: viash-io/viash-actions/pro/build-nextflow-schemas@v4
-      with:
-        components: src
-        workflows: src
-        viash_pro_token: ${{ secrets.GITHUB_TOKEN }}
-        tools_version: 'main_build'
+    # - name: Build nextflow schemas
+    #   uses: viash-io/viash-actions/pro/build-nextflow-schemas@v4
+    #   with:
+    #     components: src
+    #     workflows: src
+    #     viash_pro_token: ${{ secrets.GITHUB_TOKEN }}
+    #     tools_version: 'main_build'
 
-    - name: Build parameter files
-      uses: viash-io/viash-actions/pro/build-nextflow-params@v4
-      with:
-        workflows: src
-        components: src
-        viash_pro_token: ${{ secrets.GITHUB_TOKEN }}
-        tools_version: 'main_build'
+    # - name: Build parameter files
+    #   uses: viash-io/viash-actions/pro/build-nextflow-params@v4
+    #   with:
+    #     workflows: src
+    #     components: src
+    #     viash_pro_token: ${{ secrets.GTHB_PAT }}
+    #     tools_version: 'main_build'
 
     - name: Deploy to target branch
       uses: stefanzweifel/git-auto-commit-action@v5

src/bbmap_bbsplit/config.vsh.yaml

@@ -40,7 +40,7 @@ functionality:
       description: Directory with index files
     - name: "--versions"
       type: file
-      default: versions.yml
+      must_exist: false
 
     # Outputs
     - name: "--fastq_1"

src/bbmap_bbsplit/script.sh

@@ -47,13 +47,13 @@ else
 fi
 
 # Version
-read -r -d '' text <<- END_VERSIONS
-"${meta_functionality_name}":
-    bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset")
-END_VERSIONS
+
+text="${meta_functionality_name}:
+    bbmap: $(bbversion.sh | grep -v "Duplicate cpuset")"
 
 if [ -e "$par_versions" ]; then
     echo "$text" >> "$par_versions"
+    mv "$par_versions" "$par_updated_versions"
 else
-    echo "$text" > "$par_versions"
+    echo "$text" > "$par_updated_versions"
 fi

src/bedtools_genomecov/config.vsh.yaml

@@ -18,6 +18,9 @@ functionality:
     - name: "--extra_bedtools_args"
       type: string
       default: ''
+    - name: "--versions"
+      type: file
+      must_exist: false
 
     - name: "--bedgraph_forward"
       type: file
@@ -27,6 +30,10 @@ functionality:
       type: file
       default: $id.reverse.bedgraph
       direction: output
+    - name: "--updated_versions"
+      type: file
+      default: versions.yml
+      direction: output
 
   resources:
     - type: bash_script

src/bedtools_genomecov/script.sh

@@ -25,13 +25,13 @@ mv $prefix_forward.bedGraph $par_bedgraph_forward
 mv $prefix_reverse.bedGraph $par_bedgraph_reverse
 
 # Version
-read -r -d '' text <<- END_VERSIONS
-"${meta_functionality_name}":
-    bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
-END_VERSIONS
+
+text="${meta_functionality_name}:
+    bedtools: $(bedtools --version | sed -e "s/bedtools\ v//g")"
 
 if [ -e "$par_versions" ]; then
     echo "$text" >> "$par_versions"
+    mv "$par_versions" "$par_updated_versions"
 else
-    echo "$text" > "$par_versions"
+    echo "$text" > "$par_updated_versions"
 fi

src/cat_additional_fasta/config.vsh.yaml

@@ -22,6 +22,9 @@ functionality:
     - name: "--biotype"
       type: string
       description: Biotype value to use when appending entries to GTF file when additional fasta file is provided.
+    - name: "--versions"
+      type: file
+      must_exist: false
 
     # Output
     - name: "--fasta_output"
@@ -32,6 +35,10 @@ functionality:
       type: file
       direction: output
       description: Concatenated GTF file.
+    - name: "--updated_versions"
+      type: file
+      default: versions.yml
+      direction: output
 
   resources:
     - type: bash_script

src/cat_additional_fasta/script.sh

@@ -15,13 +15,13 @@ cat $par_fasta $par_additional_fasta > $par_fasta_output
 cat $par_gtf ${add_name%%.*}.gtf > $par_gtf_output
 
 # Version
-read -r -d '' text <<- END_VERSIONS
-"${meta_functionality_name}":
-  python: \$(python --version | sed 's/Python //g')
-END_VERSIONS
+
+text="${meta_functionality_name}:
+  python: $(python3 --version | sed 's/Python //g')"
 
 if [ -e "$par_versions" ]; then
     echo "$text" >> "$par_versions"
+    mv "$par_versions" "$par_updated_versions"
 else
-    echo "$text" > "$par_versions"
+    echo "$text" > "$par_updated_versions"
 fi

src/cat_fastq/config.vsh.yaml

@@ -18,6 +18,9 @@ functionality:
       multiple: true
       multiple_sep: ";"
       description: Read 2 fastq files to be concatenated
+    - name: "--versions"
+      type: file
+      must_exist: false
 
     - name: "--fastq_1"
       type: file
@@ -30,6 +33,10 @@ functionality:
       must_exist: false
       default: $id.read2.merged.fastq.gz
       description: Concatenated read 2 fastq
+    - name: "--updated_versions"
+      type: file
+      default: versions.yml
+      direction: output
 
   resources:
     - type: bash_script

src/cat_fastq/script.sh

@@ -16,13 +16,13 @@ if [ ${#read_2[@]} -gt 0 ]; then
 fi
 
 # Version
-read -r -d '' text <<- END_VERSIONS
-"${meta_functionality_name}":
-    cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
-END_VERSIONS
+
+text="${meta_functionality_name}:
+    cat: $(echo $(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')"
 
 if [ -e "$par_versions" ]; then
     echo "$text" >> "$par_versions"
+    mv "$par_versions" "$par_updated_versions"
 else
-    echo "$text" > "$par_versions"
+    echo "$text" > "$par_updated_versions"
 fi

src/deseq2_qc/config.vsh.yaml

@@ -29,6 +29,10 @@ functionality:
     - name: "--extra_args2"
       type: string
       default: star_salmon
+    - name: "--versions"
+      type: file
+      must_exist: false
+
 
     # OUTPUT
     - name: "--deseq2_output"
@@ -43,6 +47,10 @@ functionality:
       type: file
       direction: output
       default: deseq2.sample.dists_mqc.tsv
+    - name: "--updated_versions"
+      type: file
+      default: versions.yml
+      direction: output
 
   resources:
     - type: bash_script

src/deseq2_qc/script.sh

@@ -44,13 +44,13 @@ if [ -f "$par_deseq2_output/R_sessionInfo.log" ]; then
 fi
 
 # Version
-read -r -d '' text <<- END_VERSIONS
-"${meta_functionality_name}":
-    r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
-    bioconductor-deseq2: \$(Rscript -e "library(DESeq2); cat(as.character(packageVersion('DESeq2')))")
-END_VERSIONS
+
+text="${meta_functionality_name}:
+    r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
+    bioconductor-deseq2: $(Rscript -e 'library(DESeq2); cat(as.character(packageVersion('DESeq2')))')"
 if [ -e "$par_versions" ]; then
     echo "$text" >> "$par_versions"
+    mv "$par_versions" "$par_updated_versions"
 else
-    echo "$text" > "$par_versions"
+    echo "$text" > "$par_updated_versions"
 fi

src/dupradar/config.vsh.yaml

@@ -33,6 +33,11 @@ functionality:
       required: false
       choices: ["forward", "reverse", "unstranded"]
       description: strandedness of input bam file reads (forward, reverse or unstranded (default, applicable to paired reads))
+
+    - name: "--versions"
+      type: file
+      must_exist: false
+
 
     - name: "--output_dupmatrix"
       type: file
@@ -89,6 +94,11 @@ functionality:
       must_exist: true
       default: $id.intercept_slope.txt
       description: output file (txt) with progression of duplication rate value 
+
+    - name: "--updated_versions"
+      type: file
+      default: versions.yml
+      direction: output
 
   resources:
     - type: bash_script

src/dupradar/script.sh

@@ -28,14 +28,14 @@ mv "$par_id"_expressionHist.pdf $par_output_expression_histogram
 mv "$par_id"_intercept_slope.txt $par_output_intercept_slope
 
 # Version
-read -r -d '' text <<- END_VERSIONS
-"${meta_functionality_name}":
-    r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
-    bioconductor-dupradar: \$(Rscript -e "library(dupRadar); cat(as.character(packageVersion('dupRadar')))")
-END_VERSIONS
+
+text="${meta_functionality_name}:
+    r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
+    bioconductor-dupradar: $(Rscript -e 'library(dupRadar); cat(as.character(packageVersion('dupRadar')))')"
 
 if [ -e "$par_versions" ]; then
     echo "$text" >> "$par_versions"
+    mv "$par_versions" "$par_updated_versions"
 else
-    echo "$text" > "$par_versions"
+    echo "$text" > "$par_updated_versions"
 fi

src/fastqc/config.vsh.yaml

@@ -21,6 +21,10 @@ functionality:
       multiple_sep: ","
       description: Input fastq files, either one or two (paired)
       example: sample.fastq
+    - name: "--versions"
+      type: file
+      must_exist: false
+
 
     - name: "--fastqc_html_1"
       type: file
@@ -46,10 +50,15 @@ functionality:
       required: false
       must_exist: false
       default: $id.$key.read2.zip
+    - name: "--updated_versions"
+      type: file
+      default: versions.yml
+      direction: output
 
   resources:
     - type: bash_script
       path: script.sh
+
   test_resources:
     - type: bash_script
       path: test.sh

src/fastqc/script.sh

@@ -54,13 +54,13 @@ if [ -e "$zip2" ]; then
 fi
 
 # Version
-read -r -d '' text <<- END_VERSIONS
-"${meta_functionality_name}":
-  fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
-END_VERSIONS
+
+text="${meta_functionality_name}:
+  fastqc: $( fastqc --version | sed -e 's/FastQC v//g' )"
 
 if [ -e "$par_versions" ]; then
     echo "$text" >> "$par_versions"
+    mv "$par_versions" "$par_updated_versions"
 else
-    echo "$text" > "$par_versions"
+    echo "$text" > "$par_updated_versions"
 fi

src/fq_subsample/config.vsh.yaml

@@ -18,6 +18,10 @@ functionality:
       type: string
       default: ""
       description: Extra arguments to pass to fq subsample
+    - name: "--versions"
+      type: file
+      must_exist: false
+
 
     - name: "--output_1"
       type: file
@@ -30,6 +34,10 @@ functionality:
       direction: output
       default: $id.read2.subsampled.fastq.gz
       description: Sampled read 2 fastq files
+    - name: "--updated_versions"
+      type: file
+      default: versions.yml
+      direction: output
 
   resources:
     - type: bash_script

src/fq_subsample/script.sh

@@ -24,13 +24,13 @@ else
 fi
 
 # Version
-read -r -d '' text <<- END_VERSIONS
-"${meta_functionality_name}":
-    fq: \$(echo \$(fq subsample --version | sed 's/fq-subsample //g'))
-END_VERSIONS
+
+text="${meta_functionality_name}:
+    fq: $(echo $(fq subsample --version | sed 's/fq-subsample //g'))"
 
 if [ -e "$par_versions" ]; then
     echo "$text" >> "$par_versions"
+    mv "$par_versions" "$par_updated_versions"
 else
-    echo "$text" > "$par_versions"
+    echo "$text" > "$par_updated_versions"
 fi

src/getchromsizes/config.vsh.yaml

@@ -12,6 +12,10 @@ functionality:
   - name: "--fasta"
     type: file
     description: Genome fasta files
+  - name: "--versions"
+    type: file
+    must_exist: false
+
 
   # output
   - name: "--sizes"
@@ -26,6 +30,10 @@ functionality:
     type: file
     description: Optional gzip index file for compressed inputs
     direction: output
+  - name: "--updated_versions"
+    type: file
+    default: versions.yml
+    direction: output
 
   resources:
     - type: bash_script