chores: update more modules

nf-core · Nov 24, 2021 · a109e03 · a109e03
1 parent 16ccc5c
commit a109e03
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Showing 12 changed files with 323 additions and 5 deletions.
diff --git a/...-core/modules/qualimap/bamqc/functions.nf → modules/local/qualimap/bamqc/functions.nf b/...-core/modules/qualimap/bamqc/functions.nf → modules/local/qualimap/bamqc/functions.nf
diff --git a/...es/nf-core/modules/qualimap/bamqc/main.nf → modules/local/qualimap/bamqc/main.nf b/...es/nf-core/modules/qualimap/bamqc/main.nf → modules/local/qualimap/bamqc/main.nf
@@ -19,7 +19,7 @@ process QUALIMAP_BAMQC {
     }
 
     input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(bam), path(index)
     path gff
     val use_gff
 

diff --git a/...s/nf-core/modules/qualimap/bamqc/meta.yml → modules/local/qualimap/bamqc/meta.yml b/...s/nf-core/modules/qualimap/bamqc/meta.yml → modules/local/qualimap/bamqc/meta.yml
diff --git a/modules/nf-core/modules/tabix/bgziptabix/functions.nf b/modules/nf-core/modules/tabix/bgziptabix/functions.nf
diff --git a/modules/nf-core/modules/tabix/bgziptabix/main.nf b/modules/nf-core/modules/tabix/bgziptabix/main.nf
diff --git a/modules/nf-core/modules/tabix/bgziptabix/meta.yml b/modules/nf-core/modules/tabix/bgziptabix/meta.yml
diff --git a/modules/nf-core/modules/tabix/tabix/functions.nf b/modules/nf-core/modules/tabix/tabix/functions.nf
diff --git a/modules/nf-core/modules/tabix/tabix/main.nf b/modules/nf-core/modules/tabix/tabix/main.nf
diff --git a/modules/nf-core/modules/tabix/tabix/meta.yml b/modules/nf-core/modules/tabix/tabix/meta.yml
diff --git a/subworkflows/nf-core/ensemblvep_annotate.nf b/subworkflows/nf-core/ensemblvep_annotate.nf
diff --git a/subworkflows/nf-core/markduplicates.nf b/subworkflows/nf-core/markduplicates.nf
diff --git a/subworkflows/nf-core/snpeff_annotate.nf b/subworkflows/nf-core/snpeff_annotate.nf