Merge pull request #88 from nf-core/fix-software-version-reporting

Fix software version reporting
nf-core · Aug 15, 2024 · 716e92c · 716e92c
2 parents f0184f9 + 8a87ace
commit 716e92c
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Showing 5 changed files with 8 additions and 6 deletions.
diff --git a/modules/local/chord/main.nf b/modules/local/chord/main.nf
@@ -70,8 +70,8 @@ process CHORD {
 
     sink('versions.yml')
     writeLines('"${task.process}":')
-    writeLines(paste('    CHORD:', packageVersion('CHORD')))
-    writeLines(paste('    mutSigExtractor:', packageVersion('mutSigExtractor')))
+    writeLines(paste('    chord:', packageVersion('CHORD')))
+    writeLines(paste('    mutsigextractor:', packageVersion('mutSigExtractor')))
     sink()
     """
 

diff --git a/modules/local/linxreport/main.nf b/modules/local/linxreport/main.nf
@@ -37,7 +37,7 @@ process LINXREPORT {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        R: \$(R --version | head -n1 | sed 's/^R version \\([0-9.]\\+\\).\\+/\\1/')
+        r: \$(R --version | head -n1 | sed 's/^R version \\([0-9.]\\+\\).\\+/\\1/')
         linxreport: \$(linxreport.R --version)
     END_VERSIONS
     """

diff --git a/subworkflows/local/read_processing/main.nf b/subworkflows/local/read_processing/main.nf
@@ -92,6 +92,8 @@ workflow READ_PROCESSING {
         has_umis,
     )
 
+    ch_versions = ch_versions.mix(MARKDUPS.out.versions)
+
     // Sort into a tumor and normal channel
     ch_markdups_out = MARKDUPS.out.bam
         .branch { meta_markdups, bam, bai ->

diff --git a/workflows/targeted.nf b/workflows/targeted.nf
@@ -99,6 +99,8 @@ workflow TARGETED {
     hmf_data = PREPARE_REFERENCE.out.hmf_data
     panel_data = PREPARE_REFERENCE.out.panel_data
 
+    ch_versions = ch_versions.mix(PREPARE_REFERENCE.out.versions)
+
     // Set GRIDSS config
     gridss_config = params.gridss_config !== null ? file(params.gridss_config) : hmf_data.gridss_config
 

diff --git a/workflows/wgts.nf b/workflows/wgts.nf
@@ -104,9 +104,7 @@ workflow WGTS {
     ref_data = PREPARE_REFERENCE.out
     hmf_data = PREPARE_REFERENCE.out.hmf_data
 
-    ch_versions = ch_versions.mix(
-        PREPARE_REFERENCE.out.versions,
-    )
+    ch_versions = ch_versions.mix(PREPARE_REFERENCE.out.versions)
 
     // Set GRIDSS config
     gridss_config = params.gridss_config !== null ? file(params.gridss_config) : hmf_data.gridss_config