Merge pull request #94 from tkchafin/ci

fix bug/ CI failure in alignment subworkflow
sanger-tol · Dec 16, 2024 · 9693233 · 9693233
2 parents 159152e + cd6ccd1
commit 9693233
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Showing 8 changed files with 4,797 additions and 2 deletions.
diff --git a/lsf_error.622473.txt b/lsf_error.622473.txt
@@ -0,0 +1 @@
+Nextflow 24.10.2 is available - Please consider updating your version to it
diff --git a/lsf_error.623156.txt b/lsf_error.623156.txt
@@ -0,0 +1 @@
+Nextflow 24.10.2 is available - Please consider updating your version to it
diff --git a/lsf_error.623571.txt b/lsf_error.623571.txt
@@ -0,0 +1 @@
+Nextflow 24.10.2 is available - Please consider updating your version to it
diff --git a/lsf_output.622473.txt b/lsf_output.622473.txt
diff --git a/lsf_output.623156.txt b/lsf_output.623156.txt
diff --git a/lsf_output.623571.txt b/lsf_output.623571.txt
diff --git a/subworkflows/local/align_pacbio.nf b/subworkflows/local/align_pacbio.nf
@@ -25,7 +25,7 @@ workflow ALIGN_PACBIO {
 
 
     // Align Fastq to Genome
-    MINIMAP2_ALIGN ( FILTER_PACBIO.out.fastq, fasta, true, false, false )
+    MINIMAP2_ALIGN ( FILTER_PACBIO.out.fastq, fasta, true, false, false, false )
     ch_versions = ch_versions.mix ( MINIMAP2_ALIGN.out.versions.first() )
 
 

diff --git a/subworkflows/local/filter_pacbio.nf b/subworkflows/local/filter_pacbio.nf
@@ -33,7 +33,7 @@ workflow FILTER_PACBIO {
 
 
     // Collate BAM file to create interleaved FASTA
-    SAMTOOLS_COLLATE ( SAMTOOLS_CONVERT.out.bam, [] )
+    SAMTOOLS_COLLATE ( SAMTOOLS_CONVERT.out.bam, [[],[]] )
     ch_versions = ch_versions.mix ( SAMTOOLS_COLLATE.out.versions.first() )
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		@@ -0,0 +1 @@
		Nextflow 24.10.2 is available - Please consider updating your version to it