Merge pull request #84 from LaurenceKuhl/dev2

Add software versions
nf-core · Nov 10, 2023 · cea1e19 · cea1e19
2 parents ac50985 + 3818dd2
commit cea1e19
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Showing 6 changed files with 66 additions and 10 deletions.
diff --git a/modules/local/bagel2/bf.nf b/modules/local/bagel2/bf.nf
@@ -16,7 +16,7 @@ process BAGEL2_BF {
 
     output:
     tuple val(meta), path("*.bf"), emit: bf
-    //path "versions.yml"           , emit: versions
+    path "versions.yml"          , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -28,6 +28,11 @@ process BAGEL2_BF {
     """
     BAGEL.py bf -i $foldchange -o '${meta.treatment}_vs_${meta.reference}.bf' $args -e $reference_essentials -n $reference_nonessentials -c ${meta.treatment}
 
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
+        BAGEL2: \$( BAGEL.py version | grep -o 'Version: [0-9.]*' | awk '{print  \$2}' | grep -v '^\$')
+    END_VERSIONS
     """
 
 }
diff --git a/modules/local/bagel2/fc.nf b/modules/local/bagel2/fc.nf
@@ -11,9 +11,9 @@ process BAGEL2_FC {
     tuple val(meta), path(count_table)
 
     output:
-    tuple val(meta), path("*.foldchange"), emit: foldchange
-    tuple val(meta), path("*.normed_readcount"), emit: normed_counts
-    //path "versions.yml"           , emit: versions
+    tuple val(meta), path("*.foldchange")        , emit: foldchange
+    tuple val(meta), path("*.normed_readcount")  , emit: normed_counts
+    path "versions.yml"                          , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -24,7 +24,11 @@ process BAGEL2_FC {
 
     """
     BAGEL.py fc -i $count_table -o ${meta.treatment}_vs_${meta.reference} -c $meta.reference $args
-
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
+        BAGEL2: \$( BAGEL.py version | grep -o 'Version: [0-9.]*' | awk '{print  \$2}' | grep -v '^\$')
+    END_VERSIONS
     """
 
 }
diff --git a/modules/local/bagel2/graph.nf b/modules/local/bagel2/graph.nf
@@ -13,7 +13,7 @@ process BAGEL2_GRAPH {
 
     output:
     path("*.png")                   , emit: pictures
-
+    path "versions.yml"             , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -60,6 +60,16 @@ process BAGEL2_GRAPH {
     plt.savefig(file_name)
     plt.show()
 
+    # Output version information
+    version = pd. __version__
+    matplotlib_version = plt.matplotlib.__version__
+    # alas, no `pyyaml` pre-installed in the cellranger container
+    with open("versions.yml", "w") as f:
+        f.write('"${task.process}":\\n')
+        f.write(f'  pandas: "{version}"\\n')
+        f.write(f'  matplotlib.pyplot: "{matplotlib_version}"\\n')
+
+
     """
 
 

diff --git a/modules/local/bagel2/pr.nf b/modules/local/bagel2/pr.nf
@@ -13,8 +13,7 @@ process BAGEL2_PR {
 
     output:
     tuple val(meta), path("*.pr")   , emit: pr
-
-    //path "versions.yml"           , emit: versions
+    path "versions.yml"             , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,6 +24,12 @@ process BAGEL2_PR {
 
     """
     BAGEL.py pr -i $bf  -o '${meta.treatment}_vs_${meta.reference}.pr' -e $reference_essentials -n $reference_nonessentials
+
+    cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            python: \$(python --version | sed 's/Python //g')
+            BAGEL2: \$( BAGEL.py version | grep -o 'Version: [0-9.]*' | awk '{print  \$2}' | grep -v '^\$')
+    END_VERSIONS
     """
 
 }
diff --git a/modules/local/mageck/graphrra.nf b/modules/local/mageck/graphrra.nf
@@ -12,7 +12,7 @@ process MAGECK_GRAPHRRA {
 
     output:
     tuple val(meta), path("*.png"), emit: graphs
-
+    path "versions.yml"           , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -48,6 +48,21 @@ process MAGECK_GRAPHRRA {
     print(p1)
     dev.off()
 
+    version_file_path <- "versions.yml"
+    version_flute <- paste(unlist(packageVersion("MAGeCKFlute")), collapse = ".")
+    version_ggplot <- paste(unlist(packageVersion("MAGeCKFlute")), collapse = ".")
+
+    f <- file(version_file_path, "w")
+    writeLines('"${task.process}":', f)
+    writeLines("    MAGeCKFlute: ", f, sep = "")
+    writeLines(version_flute, f)
+    writeLines("    ggplot2: ", f, sep = "")
+    writeLines(version_ggplot, f)
+    close(f)
+
+
+
+
     """
 
 

diff --git a/workflows/crisprseq_screening.nf b/workflows/crisprseq_screening.nf
@@ -116,7 +116,7 @@ workflow CRISPRSEQ_SCREENING {
             [[id: condition, single_end: single_end], fastqs]
         }
         .set { joined }
-        joined.dump(tag:"metadata")
+
 
         //
         // MODULE: Run mageck count
@@ -147,6 +147,9 @@ workflow CRISPRSEQ_SCREENING {
             params.min_targeted_genes
         )
 
+        ch_versions = ch_versions.mix(CRISPRCLEANR_NORMALIZE.out.versions)
+
+
         CRISPRCLEANR_NORMALIZE.out.norm_count_file.map {
             it -> it[1]
         }.set { ch_counts }
@@ -162,9 +165,12 @@ workflow CRISPRSEQ_SCREENING {
             counts
         )
 
+        ch_versions = ch_versions.mix(MAGECK_TEST.out.versions)
+
         MAGECK_GRAPHRRA (
             MAGECK_TEST.out.gene_summary
         )
+        ch_versions = ch_versions.mix(MAGECK_GRAPHRRA.out.versions)
     }
 
     if(params.rra_contrasts) {
@@ -180,19 +186,26 @@ workflow CRISPRSEQ_SCREENING {
     BAGEL2_FC (
             counts
         )
+    ch_versions = ch_versions.mix(BAGEL2_FC.out.versions)
 
     BAGEL2_BF (
         BAGEL2_FC.out.foldchange,
         ch_bagel_reference_essentials,
         ch_bagel_reference_nonessentials
     )
 
+    ch_versions = ch_versions.mix(BAGEL2_BF.out.versions)
+
+
     ch_bagel_pr = BAGEL2_BF.out.bf.combine(ch_bagel_reference_essentials)
                                         .combine(ch_bagel_reference_nonessentials)
 
     BAGEL2_PR (
         ch_bagel_pr
     )
+
+    ch_versions = ch_versions.mix(BAGEL2_PR.out.versions)
+
     BAGEL2_GRAPH (
         BAGEL2_PR.out.pr
     )
@@ -207,6 +220,10 @@ workflow CRISPRSEQ_SCREENING {
         MAGECK_MLE (
             ch_designed_mle
         )
+
+        ch_versions = ch_versions.mix(MAGECK_MLE.out.versions)
+
+
     }
 
     CUSTOM_DUMPSOFTWAREVERSIONS (