Pass empty meta for modules needing it

nf-core · Feb 1, 2024 · da58939 · da58939
1 parent 12b6e43
commit da58939
Showing 1 changed file with 33 additions and 5 deletions.
diff --git a/workflows/chipseq.nf b/workflows/chipseq.nf
@@ -173,7 +173,12 @@ workflow CHIPSEQ {
             FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.reads,
             PREPARE_GENOME.out.bwa_index,
             false,
-            PREPARE_GENOME.out.fasta
+            PREPARE_GENOME
+                .out
+                .fasta
+                .map {
+                        [ [:], it ]
+                }
         )
         ch_genome_bam        = FASTQ_ALIGN_BWA.out.bam
         ch_genome_bam_index  = FASTQ_ALIGN_BWA.out.bai
@@ -193,6 +198,9 @@ workflow CHIPSEQ {
             params.save_unaligned,
             false,
             PREPARE_GENOME.out.fasta
+                .map {
+                        [ [:], it ]
+                }
         )
         ch_genome_bam        = FASTQ_ALIGN_BOWTIE2.out.bam
         ch_genome_bam_index  = FASTQ_ALIGN_BOWTIE2.out.bai
@@ -209,7 +217,9 @@ workflow CHIPSEQ {
         FASTQ_ALIGN_CHROMAP (
             FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.reads,
             PREPARE_GENOME.out.chromap_index,
-            PREPARE_GENOME.out.fasta
+            PREPARE_GENOME
+                .out
+                .fasta
                 .map {
                     [ [:], it ]
                 },
@@ -233,7 +243,12 @@ workflow CHIPSEQ {
         ALIGN_STAR (
             FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.reads,
             PREPARE_GENOME.out.star_index,
-            PREPARE_GENOME.out.fasta,
+            PREPARE_GENOME
+                .out
+                .fasta
+                .map {
+                        [ [:], it ]
+                },
             params.seq_center ?: ''
         )
         ch_genome_bam        = ALIGN_STAR.out.bam
@@ -275,8 +290,16 @@ workflow CHIPSEQ {
     //
     BAM_MARKDUPLICATES_PICARD (
         PICARD_MERGESAMFILES.out.bam,
-        PREPARE_GENOME.out.fasta,
+        PREPARE_GENOME
+            .out
+            .fasta
+            .map {
+                    [ [:], it ]
+            },
         PREPARE_GENOME.out.fai
+            .map {
+                [ [:], it ]
+            }
     )
     ch_versions = ch_versions.mix(BAM_MARKDUPLICATES_PICARD.out.versions)
 
@@ -286,7 +309,12 @@ workflow CHIPSEQ {
     BAM_FILTER_BAMTOOLS (
         BAM_MARKDUPLICATES_PICARD.out.bam.join(BAM_MARKDUPLICATES_PICARD.out.bai, by: [0]),
         PREPARE_GENOME.out.filtered_bed.first(),
-        PREPARE_GENOME.out.fasta,
+        PREPARE_GENOME
+            .out
+            .fasta
+            .map {
+                [ [:], it ]
+            },
         ch_bamtools_filter_se_config,
         ch_bamtools_filter_pe_config
     )