Merge pull request #3 from mirpedrol/dev2

Dev2
LaurenceKuhl · Nov 13, 2023 · 43ce6cd · 43ce6cd
2 parents c8ad5a2 + ea081e0
commit 43ce6cd
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Showing 7 changed files with 34 additions and 8 deletions.
diff --git a/modules/local/alignment_summary.nf b/modules/local/alignment_summary.nf
@@ -12,6 +12,7 @@ process ALIGNMENT_SUMMARY {
 
     output:
     tuple val(meta), path("*_alignment_summary.csv"), emit: summary
+    path "versions.yml",                              emit: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/modules/local/cigar_parser.nf b/modules/local/cigar_parser.nf
@@ -41,7 +41,13 @@ process CIGAR_PARSER {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        Rscript: \$(Rscript --version)
+        seqinr: \$(Rscript -e "cat(paste(packageVersion('seqinr'), collapse='.'))")
+        Rsamtools: \$(Rscript -e "cat(paste(packageVersion('Rsamtools'), collapse='.'))")
+        dplyr: \$(Rscript -e "cat(paste(packageVersion('dplyr'), collapse='.'))")
+        ShortRead: \$(Rscript -e "cat(paste(packageVersion('ShortRead'), collapse='.'))")
+        jsonlite: \$(Rscript -e "cat(paste(packageVersion('jsonlite'), collapse='.'))")
+        stringr: \$(Rscript -e "cat(paste(packageVersion('stringr'), collapse='.'))")
+        plotly: \$(Rscript -e "cat(paste(packageVersion('plotly'), collapse='.'))")
     END_VERSIONS
     """
 }
diff --git a/modules/local/crisprseq_plotter.nf b/modules/local/crisprseq_plotter.nf
@@ -35,7 +35,19 @@ process CRISPRSEQ_PLOTTER {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        Rscript: \$(Rscript --version)
+        ggplot2: \$(Rscript -e "cat(paste(packageVersion('ggplot2'), collapse='.'))")
+        ShortRead: \$(Rscript -e "cat(paste(packageVersion('ShortRead'), collapse='.'))")
+        plyr: \$(Rscript -e "cat(paste(packageVersion('plyr'), collapse='.'))")
+        dplyr: \$(Rscript -e "cat(paste(packageVersion('dplyr'), collapse='.'))")
+        seqinr: \$(Rscript -e "cat(paste(packageVersion('seqinr'), collapse='.'))")
+        ggpubr: \$(Rscript -e "cat(paste(packageVersion('ggpubr'), collapse='.'))")
+        ggmsa: \$(Rscript -e "cat(paste(packageVersion('ggmsa'), collapse='.'))")
+        seqmagick: \$(Rscript -e "cat(paste(packageVersion('seqmagick'), collapse='.'))")
+        stringr: \$(Rscript -e "cat(paste(packageVersion('stringr'), collapse='.'))")
+        tidyr: \$(Rscript -e "cat(paste(packageVersion('tidyr'), collapse='.'))")
+        ggseqlogo: \$(Rscript -e "cat(paste(packageVersion('ggseqlogo'), collapse='.'))")
+        plotly: \$(Rscript -e "cat(paste(packageVersion('plotly'), collapse='.'))")
+        cowplot: \$(Rscript -e "cat(paste(packageVersion('cowplot'), collapse='.'))")
     END_VERSIONS
     """
 }
diff --git a/templates/alignment_summary.py b/templates/alignment_summary.py
@@ -22,3 +22,7 @@
             add_line = False
     if add_line:
         output_file.write(f"aligned-reads, {mapped_reads_count} ({round(mapped_reads_percentage, 1)}%)\\n")
+
+with open("versions.yml", "w") as f:
+    f.write('"${task.process}":\\n')
+    f.write(f'  pysam: "{pysam.__version__}"\\n')
diff --git a/templates/clustering_summary.py b/templates/clustering_summary.py
@@ -3,6 +3,7 @@
 import gzip
 import sys
 
+import Bio
 from Bio import SeqIO
 
 with gzip.open("$reads", "rt") as handle:
@@ -25,3 +26,4 @@
 
 with open("versions.yml", "w") as f:
     f.write('"${task.process}":\\n')
+    f.write(f'  biopython: "{Bio.__version__}"\\n')
diff --git a/templates/preprocessing_summary.py b/templates/preprocessing_summary.py
@@ -2,6 +2,7 @@
 
 import gzip
 
+import Bio
 from Bio import SeqIO
 
 with gzip.open("${raw_reads[0]}", "rt") as handle:
@@ -50,10 +51,7 @@
             f"quality-filtered-reads, {trimmed_reads_count} ({round(trimmed_reads_count * 100 / assembled_reads_count,1)}%)\\n"
         )
 
-    # 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')
 
+with open("versions.yml", "w") as f:
+    f.write('"${task.process}":\\n')
+    f.write(f'  biopython: "{Bio.__version__}"\\n')
diff --git a/workflows/crisprseq_targeted.nf b/workflows/crisprseq_targeted.nf
@@ -370,6 +370,7 @@ workflow CRISPRSEQ_TARGETED {
     PREPROCESSING_SUMMARY {
         ch_preprocessing_summary_data
     }
+    ch_versions = ch_versions.mix(PREPROCESSING_SUMMARY.out.versions)
 
 
     if (params.umi_clustering) {
@@ -663,6 +664,7 @@ workflow CRISPRSEQ_TARGETED {
         ch_mapped_bam
             .join(CLUSTERING_SUMMARY.out.summary)
     )
+    ch_versions = ch_versions.mix(ALIGNMENT_SUMMARY.out.versions)
 
 
     //
@@ -705,6 +707,7 @@ workflow CRISPRSEQ_TARGETED {
             }
     }
     .set { ch_template_bam }
+    ch_versions = ch_versions.mix(MINIMAP2_ALIGN_TEMPLATE.out.versions)
 
     ch_mapped_bam
         .join(SAMTOOLS_INDEX.out.bai)
-Original file line number
+Diff line change
@@ Expand Up / @@ -12,6 +12,7 @@ process ALIGNMENT_SUMMARY { @@
         output:
         tuple val(meta), path("*_alignment_summary.csv"), emit: summary
+        path "versions.yml",                              emit: versions
         when:
         task.ext.when == null || task.ext.when
@@ Expand Down @@