fix joining

nf-core · Nov 23, 2023 · b75a8f7 · b75a8f7
1 parent 6bf0a4e
commit b75a8f7
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Showing 2 changed files with 6 additions and 6 deletions.
diff --git a/subworkflows/local/bam_merge_index_samtools/main.nf b/subworkflows/local/bam_merge_index_samtools/main.nf
@@ -25,14 +25,14 @@ workflow BAM_MERGE_INDEX_SAMTOOLS {
     // Only when using intervals
     MERGE_BAM(bam_to_merge.multiple, [ [ id:'null' ], []], [ [ id:'null' ], []])
 
-    // Mix intervals and no_intervals channels together
+    // Join with the bai file
     bam_bai_merged = MERGE_BAM.out.bam.join(MERGE_BAM.out.bai, failOnDuplicate: true, failOnMismatch: true)
 
     // Index single bams, merged ones are indexed on the fly
     INDEX_MERGE_BAM(bam_to_merge.single)
     bam_bai_single = bam_to_merge.single.join(INDEX_MERGE_BAM.out.bai, failOnDuplicate: true, failOnMismatch: true)
 
-    // Join with the bai file
+    // Mix intervals and no_intervals channels together
     bam_bai = bam_bai_merged.mix(bam_bai_single)
 
     // Gather versions of all tools used

diff --git a/subworkflows/local/cram_merge_index_samtools/main.nf b/subworkflows/local/cram_merge_index_samtools/main.nf
@@ -27,14 +27,14 @@ workflow CRAM_MERGE_INDEX_SAMTOOLS {
     // Only when using intervals
     MERGE_CRAM(cram_to_merge.multiple, fasta.map{ it -> [ [ id:'fasta' ], it ] }, fasta_fai.map{ it -> [ [ id:'fasta_fai' ], it ] })
 
-    // Mix intervals and no_intervals channels together
+    // Join with the crai file
     cram_crai_merged = MERGE_CRAM.out.cram.join(MERGE_CRAM.out.crai, failOnDuplicate: true, failOnMismatch: true)
 
-    // Index cram
+    // Index cram, multiple ones are indexed on the fly
     INDEX_CRAM(cram_to_merge.single)
-    cram_crai_single = cram_to_merge.single.join(INDEX_CRAM.out.bai, failOnDuplicate: true, failOnMismatch: true)
+    cram_crai_single = cram_to_merge.single.join(INDEX_CRAM.out.crai, failOnDuplicate: true, failOnMismatch: true)
 
-    // Join with the crai file
+    // Mix intervals and no_intervals channels together
     cram_crai = cram_crai_merged.mix(cram_crai_single)
 
     // Gather versions of all tools used