Fix bcftools merge (genomic-medicine-sweden#43)

Fix bcftools merge --------- Co-authored-by: Anders Jemt <[email protected]>
fellen31 · Mar 27, 2024 · 6f9f9e4 · 6f9f9e4
1 parent dac7bee
commit 6f9f9e4
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -15,6 +15,8 @@ Initial release of genomic-medicine-sweden/skierfe, created with the [nf-core](h
 
 ### `Fixed`
 
+- Fix BCFTools merge module inputs [#43](https://github.com/genomic-medicine-sweden/skierfe/pull/43)
+
 ### `Dependencies`
 
 ### `Deprecated`
diff --git a/conf/modules/repeat_calling.config b/conf/modules/repeat_calling.config
@@ -66,9 +66,11 @@ process {
     }
 
     withName: BCFTOOLS_MERGE {
-        ext.args = "--output-type b"
+
+        ext.args = '--output-type b'
+
         publishDir = [
-            path: { "${params.outdir}/repeat_analysis/trgt/processed/${meta.id}" },
+            path: { "${params.outdir}/repeat_analysis/bcftools/merge/${meta.id}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]

diff --git a/modules.json b/modules.json
@@ -18,8 +18,7 @@
                     "bcftools/merge": {
                         "branch": "master",
                         "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/bcftools/merge/bcftools-merge.diff"
+                        "installed_by": ["modules"]
                     },
                     "bcftools/norm": {
                         "branch": "master",

diff --git a/modules/nf-core/bcftools/merge/bcftools-merge.diff b/modules/nf-core/bcftools/merge/bcftools-merge.diff
diff --git a/modules/nf-core/bcftools/merge/main.nf b/modules/nf-core/bcftools/merge/main.nf
diff --git a/subworkflows/local/repeat_analysis.nf b/subworkflows/local/repeat_analysis.nf
@@ -34,33 +34,14 @@ workflow REPEAT_ANALYSIS {
 
     BCFTOOLS_SORT_TRGT.out.vcf
         .join(BCFTOOLS_INDEX_TRGT.out.csi)
-        .set{ ch_bcftools_query_in }
-
-    ch_bcftools_query_in
-        .map{[['id':'multisample'],it[1]]}
-        .groupTuple()
-        .set{ vcfs }
-
-    ch_bcftools_query_in
-        .map{[['id':'multisample'],it[2]]}
+        .toList()
+        .filter { it.size() > 1 }
+        .flatMap()
+        .map { meta, bcf, csi -> [ [ id : 'multisample' ], bcf, csi ] }
         .groupTuple()
-        .set{ csis }
-
-    vcfs
-        .cross(csis)
-        .map{[it[0][0], it[0][1], it[1][1]]}
-        .set{ch_bcftools_merge_in}
-
-    // BCFTools merge fails if only one file is provided in arguments,
-    // therefore make a list of all files to be merged and provide it
-
-    ch_bcftools_merge_in
-        .map{ meta, vcf, index -> vcf.name.toString().replaceAll("[\\[\\]]", "") }
-        .collectFile(name: 'bcftools_merge_samples.txt', newLine: true)
-        .map{ file_list -> [ [:], file_list ] }
-        .set{ ch_bcftools_file_list }
+        .set{ ch_bcftools_merge_in }
 
-    BCFTOOLS_MERGE(ch_bcftools_merge_in, ch_fasta, ch_fai, [], ch_bcftools_file_list )
+    BCFTOOLS_MERGE ( ch_bcftools_merge_in, ch_fasta, ch_fai, [] )
 
     ch_versions = ch_versions.mix(TRGT.out.versions)
     ch_versions = ch_versions.mix(SAMTOOLS_SORT_TRGT.out.versions)