Added versions snippet to multiple modules

Plant-Food-Research-Open · Feb 26, 2024 · 1dd2e26 · 1dd2e26
1 parent 1b2632f
commit 1dd2e26
Show file tree

Hide file tree

Showing 10 changed files with 95 additions and 18 deletions.
diff --git a/modules/local/agp2assembly.nf b/modules/local/agp2assembly.nf
@@ -9,13 +9,20 @@ process AGP2ASSEMBLY {
 
     output:
     tuple val(sample_id_on_tag), path("*.agp.assembly"), emit: assembly
+    path "versions.yml"                                , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
+    def VERSION = '0.1.0'
     """
     assembly_tag=\$(echo $sample_id_on_tag | sed 's/.*\\.on\\.//g')
     agp2assembly.py $agp_file "\${assembly_tag}.agp.assembly"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        juicebox_scripts: $VERSION
+    END_VERSIONS
     """
 }
diff --git a/modules/local/assembly2bedpe.nf b/modules/local/assembly2bedpe.nf
@@ -8,7 +8,8 @@ process ASSEMBLY2BEDPE {
     tuple val(sample_id_on_tag), path(agp_assembly_file)
 
     output:
-    tuple val(sample_id_on_tag), path("*.assembly.bedpe"), emit: bedpe
+    tuple val(sample_id_on_tag), path("*.assembly.bedpe")   , emit: bedpe
+    path "versions.yml"                                     , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -17,11 +18,23 @@ process ASSEMBLY2BEDPE {
     """
     assembly_tag=\$(echo $sample_id_on_tag | sed 's/.*\\.on\\.//g')
     assembly2bedpe.py $agp_assembly_file > "\${assembly_tag}.assembly.bedpe"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | tr -d 'Python[:space:]')
+        pandas: \$(python -c "import pandas; print(pandas.__version__)")
+    END_VERSIONS
     """
 
     stub:
     """
     assembly_tag=\$(echo $sample_id_on_tag | sed 's/.*\\.on\\.//g')
     touch "\${assembly_tag}.assembly.bedpe"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | tr -d 'Python[:space:]')
+        pandas: \$(python -c "import pandas; print(pandas.__version__)")
+    END_VERSIONS
     """
 }
diff --git a/modules/local/hic2html.nf b/modules/local/hic2html.nf
@@ -8,7 +8,8 @@ process HIC2HTML {
     tuple val(sample_id_on_tag), path(hic_file)
 
     output:
-    path "*.html", emit: html
+    path "*.html"           , emit: html
+    path "versions.yml"     , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -17,5 +18,10 @@ process HIC2HTML {
     """
     file_name="$hic_file"
     hic2html.py "$hic_file" > "\${file_name%.*}.html"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | tr -d 'Python[:space:]')
+    END_VERSIONS
     """
 }
diff --git a/modules/local/juicer_sort.nf b/modules/local/juicer_sort.nf
@@ -10,7 +10,8 @@ process JUICER_SORT {
     tuple val(sample_id_on_tag), path(out_links_txt)
 
     output:
-    tuple val(sample_id_on_tag), path("*sorted.links.txt"), emit: links
+    tuple val(sample_id_on_tag), path("*sorted.links.txt")  , emit: links
+    path "versions.yml"                                     , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -21,5 +22,10 @@ process JUICER_SORT {
         -k2,2 -k6,6 \\
         $out_links_txt \\
         > out.sorted.links.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sort: \$(sort --version | sed -n '/sort (GNU coreutils) / s/sort (GNU coreutils) //p')
+    END_VERSIONS
     """
 }
diff --git a/modules/local/makeagpfromfasta.nf b/modules/local/makeagpfromfasta.nf
@@ -8,14 +8,21 @@ process MAKEAGPFROMFASTA {
     tuple val(sample_id_on_tag), path(assembly_fasta)
 
     output:
-    tuple val(sample_id_on_tag), path("*.agp"), emit: agp
+    tuple val(sample_id_on_tag), path("*.agp")  , emit: agp
+    path "versions.yml"                         , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
+    def VERSION = '0.1.0'
     """
     file_name="$assembly_fasta"
     makeAgpFromFasta.py $assembly_fasta "\${file_name%%.*}.agp"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        juicebox_scripts: $VERSION
+    END_VERSIONS
     """
 }
diff --git a/modules/local/matlock_bam2_juicer.nf b/modules/local/matlock_bam2_juicer.nf
@@ -7,16 +7,23 @@ process MATLOCK_BAM2_JUICER {
         'biocontainers/matlock:20181227--h4b03ef3_3' }"
 
     input:
-        tuple val(sample_id_on_tag), path(hic_bam_scaffolds)
+    tuple val(sample_id_on_tag), path(hic_bam_scaffolds)
 
     output:
-        tuple val(sample_id_on_tag), path("out.links.txt")
+    tuple val(sample_id_on_tag), path("out.links.txt")  , emit: links
+    path "versions.yml"                                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-        """
-        matlock bam2 juicer $hic_bam_scaffolds out.links.txt
-        """
+    def VERSION = '20181227'
+    """
+    matlock bam2 juicer $hic_bam_scaffolds out.links.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        matlock: $VERSION
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/ncbi_fcs_gx_setup_sample.nf b/modules/local/ncbi_fcs_gx_setup_sample.nf
@@ -10,7 +10,8 @@ process NCBI_FCS_GX_SETUP_SAMPLE {
     tuple val(asm_tag), path(fasta_file)
 
     output:
-    path 'fasta.file.for.*.fasta', emit: fsata
+    path 'fasta.file.for.*.fasta'   , emit: fsata
+    path "versions.yml"             , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,5 +23,10 @@ process NCBI_FCS_GX_SETUP_SAMPLE {
     }
     """
     ln -s $fasta_file "fasta.file.for.${asm_tag}.fasta"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ubuntu: \$(cat /etc/issue | tr -d 'Ubuntu LTS[:space:]\\\\')
+    END_VERSIONS
     """
 }
diff --git a/modules/local/runassemblyvisualizer.nf b/modules/local/runassemblyvisualizer.nf
@@ -8,7 +8,8 @@ process RUNASSEMBLYVISUALIZER {
     tuple val(sample_id_on_tag), path(agp_assembly_file), path(sorted_links_txt_file)
 
     output:
-    tuple val(sample_id_on_tag), path("*.hic"), emit: hic
+    tuple val(sample_id_on_tag), path("*.hic")  , emit: hic
+    path "versions.yml"                         , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -23,11 +24,21 @@ process RUNASSEMBLYVISUALIZER {
         $agp_assembly_file $sorted_links_txt_file
 
     mv "\${file_name%.*}.hic" "\${assembly_tag}.hic"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        run-assembly-visualizer.sh: \$(/usr/src/3d-dna/visualize/run-assembly-visualizer.sh -h | sed -n '/Visualizing draft genomes in juicebox:/ s/Visualizing draft genomes in juicebox: //p')
+    END_VERSIONS
     """
 
     stub:
     """
     assembly_tag=\$(echo $sample_id_on_tag | sed 's/.*\\.on\\.//g')
     touch "\${assembly_tag}.hic"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        run-assembly-visualizer.sh: \$(/usr/src/3d-dna/visualize/run-assembly-visualizer.sh -h | sed -n '/Visualizing draft genomes in juicebox:/ s/Visualizing draft genomes in juicebox: //p')
+    END_VERSIONS
     """
 }
diff --git a/subworkflows/local/fq2hic.nf b/subworkflows/local/fq2hic.nf
@@ -57,21 +57,32 @@ workflow FQ2HIC {
 
     // MODULE: MAKEAGPFROMFASTA | AGP2ASSEMBLY | ASSEMBLY2BEDPE
     MAKEAGPFROMFASTA ( ch_bam_and_ref.map { meta3, bam, fa -> [ meta3.id, fa ] } )
-    | AGP2ASSEMBLY
-    | ASSEMBLY2BEDPE
+    AGP2ASSEMBLY ( MAKEAGPFROMFASTA.out.agp )
+    ASSEMBLY2BEDPE ( AGP2ASSEMBLY.out.assembly )
+
+    ch_versions                     = ch_versions.mix(MAKEAGPFROMFASTA.out.versions.first())
+                                    | mix(AGP2ASSEMBLY.out.versions.first())
+                                    | mix(ASSEMBLY2BEDPE.out.versions.first())
 
     // MODULE: MATLOCK_BAM2_JUICER | JUICER_SORT
     MATLOCK_BAM2_JUICER ( ch_bam_and_ref.map { meta3, bam, fa -> [ meta3.id, bam ] } )
-    | JUICER_SORT
+
+    JUICER_SORT ( MATLOCK_BAM2_JUICER.out.links )
+
+    ch_versions                     = ch_versions.mix(MATLOCK_BAM2_JUICER.out.versions.first())
+                                    | mix(JUICER_SORT.out.versions.first())
 
     // MODULE: RUNASSEMBLYVISUALIZER
     RUNASSEMBLYVISUALIZER ( AGP2ASSEMBLY.out.assembly.join(JUICER_SORT.out.links) )
 
     ch_hic                          = RUNASSEMBLYVISUALIZER.out.hic
+    ch_versions                     = ch_versions.mix(RUNASSEMBLYVISUALIZER.out.versions.first())
 
     // MODULE: HIC2HTML
     HIC2HTML ( ch_hic )
 
+    ch_versions                     = ch_versions.mix(HIC2HTML.out.versions.first())
+
     emit:
     hic                             = ch_hic
     html                            = HIC2HTML.out.html

diff --git a/subworkflows/local/ncbi_fcs_gx.nf b/subworkflows/local/ncbi_fcs_gx.nf
@@ -9,12 +9,16 @@ workflow NCBI_FCS_GX {
     tax_id                  // val: Integer
 
     main:
+    ch_versions             = Channel.empty()
+
     // MODULE: NCBI_FCS_GX_SETUP_SAMPLE
     NCBI_FCS_GX_SETUP_SAMPLE ( tuple_of_tag_file )
 
     ch_all_samples          = NCBI_FCS_GX_SETUP_SAMPLE.out.fsata
                             | collect
 
+    ch_versions             = ch_versions.mix(NCBI_FCS_GX_SETUP_SAMPLE.out.versions.first())
+
     // MODULE: NCBI_FCS_GX_SCREEN_SAMPLES
     NCBI_FCS_GX_SCREEN_SAMPLES(
         ch_all_samples,
@@ -38,14 +42,13 @@ workflow NCBI_FCS_GX {
                                 [tag, it]
                             }
 
+    ch_versions             = ch_versions.mix(NCBI_FCS_GX_SCREEN_SAMPLES.out.versions)
+
     // MODULE: NCBI_FCS_GX_KRONA_PLOT
     NCBI_FCS_GX_KRONA_PLOT ( ch_gx_taxonomy )
 
     ch_gx_taxonomy_plot     = NCBI_FCS_GX_KRONA_PLOT.out.plot
-
-    ch_versions             = Channel.empty()
-                            | mix(NCBI_FCS_GX_SCREEN_SAMPLES.out.versions.first())
-                            | mix(NCBI_FCS_GX_KRONA_PLOT.out.versions.first())
+    ch_versions             = ch_versions.mix(NCBI_FCS_GX_KRONA_PLOT.out.versions.first())
 
     emit:
     gx_report               = ch_gx_report