The upstream module now has the functionality

sanger-tol · Jun 24, 2024 · d879a5f · d879a5f
1 parent 9dd4af7
commit d879a5f
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Showing 6 changed files with 43 additions and 46 deletions.
diff --git a/modules.json b/modules.json
@@ -88,9 +88,8 @@
                     },
                     "samtools/view": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/samtools/view/samtools-view.diff"
+                        "git_sha": "6c2309aaec566c0d44a6cf14d4b2d0c51afe2e91",
+                        "installed_by": ["modules"]
                     },
                     "untar": {
                         "branch": "master",

diff --git a/modules/nf-core/samtools/view/environment.yml b/modules/nf-core/samtools/view/environment.yml
diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf
diff --git a/modules/nf-core/samtools/view/meta.yml b/modules/nf-core/samtools/view/meta.yml
diff --git a/modules/nf-core/samtools/view/samtools-view.diff b/modules/nf-core/samtools/view/samtools-view.diff
diff --git a/subworkflows/local/filter_pacbio.nf b/subworkflows/local/filter_pacbio.nf
@@ -77,7 +77,7 @@ workflow FILTER_PACBIO {
 
 
     // Convert BAM to FASTQ
-    SAMTOOLS_FASTQ ( SAMTOOLS_FILTER.out.unoutput, true )
+    SAMTOOLS_FASTQ ( SAMTOOLS_FILTER.out.unselected, true )
     ch_versions = ch_versions.mix ( SAMTOOLS_FASTQ.out.versions.first() )