Merge pull request #435 from ftabaro/fix-gffread

Fix GFFREAD

Author: JoseEspinosa

CHANGELOG.md

@@ -7,7 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
-[[PR #434](https://github.com/nf-core/chipseq/pull/434)] - Prevent pipeline fails from erroneous param validation when igenomes is used.
+- [[PR #434](https://github.com/nf-core/chipseq/pull/434)] - Prevent pipeline fails from erroneous param validation when igenomes is used.
+- [[#432](https://github.com/nf-core/chipseq/issues/432)] - Fix `GFFREAD` call to have the two expected input channels.
 
 ### Parameters
 

subworkflows/local/prepare_genome.nf

@@ -3,33 +3,35 @@
 //
 
 include {
-    GUNZIP as GUNZIP_FASTA
-    GUNZIP as GUNZIP_GTF
-    GUNZIP as GUNZIP_GFF
-    GUNZIP as GUNZIP_GENE_BED
-    GUNZIP as GUNZIP_BLACKLIST } from '../../modules/nf-core/gunzip/main'
+    GUNZIP as GUNZIP_FASTA ;
+    GUNZIP as GUNZIP_GTF ;
+    GUNZIP as GUNZIP_GFF ;
+    GUNZIP as GUNZIP_GENE_BED ;
+    GUNZIP as GUNZIP_BLACKLIST
+} from '../../modules/nf-core/gunzip/main'
 
 include {
-    UNTAR as UNTAR_BWA_INDEX
-    UNTAR as UNTAR_BOWTIE2_INDEX
-    UNTAR as UNTAR_STAR_INDEX    } from '../../modules/nf-core/untar/main'
-
-include { UNTARFILES           } from '../../modules/nf-core/untarfiles/main'
-include { GFFREAD              } from '../../modules/nf-core/gffread/main'
-include { CUSTOM_GETCHROMSIZES } from '../../modules/nf-core/custom/getchromsizes/main'
-include { BWA_INDEX            } from '../../modules/nf-core/bwa/index/main'
-include { BOWTIE2_BUILD        } from '../../modules/nf-core/bowtie2/build/main'
-include { CHROMAP_INDEX        } from '../../modules/nf-core/chromap/index/main'
-
-include { GTF2BED                  } from '../../modules/local/gtf2bed'
-include { GENOME_BLACKLIST_REGIONS } from '../../modules/local/genome_blacklist_regions'
-include { STAR_GENOMEGENERATE      } from '../../modules/local/star_genomegenerate'
+    UNTAR as UNTAR_BWA_INDEX ;
+    UNTAR as UNTAR_BOWTIE2_INDEX ;
+    UNTAR as UNTAR_STAR_INDEX
+} from '../../modules/nf-core/untar/main'
+
+include { UNTARFILES                   } from '../../modules/nf-core/untarfiles/main'
+include { GFFREAD                      } from '../../modules/nf-core/gffread/main'
+include { CUSTOM_GETCHROMSIZES         } from '../../modules/nf-core/custom/getchromsizes/main'
+include { BWA_INDEX                    } from '../../modules/nf-core/bwa/index/main'
+include { BOWTIE2_BUILD                } from '../../modules/nf-core/bowtie2/build/main'
+include { CHROMAP_INDEX                } from '../../modules/nf-core/chromap/index/main'
+
+include { GTF2BED                      } from '../../modules/local/gtf2bed'
+include { GENOME_BLACKLIST_REGIONS     } from '../../modules/local/genome_blacklist_regions'
+include { STAR_GENOMEGENERATE          } from '../../modules/local/star_genomegenerate'
 
 workflow PREPARE_GENOME {
     take:
     genome             //  string: genome name
     genomes            //     map: genome attributes
-    prepare_tool_index // string  : tool to prepare index for
+    prepare_tool_index //  string: tool to prepare index for
     fasta              //    path: path to genome fasta file
     gtf                //    file: /path/to/genome.gtf
     gff                //    file: /path/to/genome.gff
@@ -49,30 +51,32 @@ workflow PREPARE_GENOME {
     //
     ch_fasta = Channel.empty()
     if (fasta.endsWith('.gz')) {
-        ch_fasta    = GUNZIP_FASTA ( [ [:], fasta ] ).gunzip.map{ it[1] }
+        ch_fasta    = GUNZIP_FASTA([[:], fasta]).gunzip.map { it[1] }
         ch_versions = ch_versions.mix(GUNZIP_FASTA.out.versions)
-    } else {
-        ch_fasta = Channel.value(file(fasta))
+    }
+    else {
+        ch_fasta = Channel.value(file(fasta, checkIfExists: true))
     }
 
     //
     // Uncompress GTF annotation file or create from GFF3 if required
     //
     if (gtf) {
         if (gtf.endsWith('.gz')) {
-            ch_gtf      = GUNZIP_GTF ( [ [:], gtf ] ).gunzip.map{ it[1] }
+            ch_gtf      = GUNZIP_GTF([[:], gtf]).gunzip.map { it[1] }
             ch_versions = ch_versions.mix(GUNZIP_GTF.out.versions)
         } else {
-            ch_gtf = Channel.value(file(gtf))
+            ch_gtf = Channel.value(file(gtf, checkIfExists: true))
         }
     } else if (gff) {
         if (gff.endsWith('.gz')) {
-            ch_gff      = GUNZIP_GFF ( [ [:], gff ] ).gunzip.map{ it[1] }
-            ch_versions = ch_versions.mix(GUNZIP_GFF.out.versions)
+            ch_gff      = GUNZIP_GFF([[:], file(gff, checkIfExists: true)]).gunzip.map { it[1] }
+            ch_versions = ch_versions.mix(GUNZIP_GFF.out.versions).map { [ [:], it ] }
         } else {
-            ch_gff = Channel.value(file(gff))
+            ch_gff = Channel.value(file(gff, checkIfExists: true))
         }
-        ch_gtf      = GFFREAD ( [ [:], ch_gff ] ).gtf
+
+        ch_gtf      = GFFREAD(ch_gff, []).gtf.map { it[1] }
         ch_versions = ch_versions.mix(GFFREAD.out.versions)
     }
 
@@ -82,7 +86,7 @@ workflow PREPARE_GENOME {
     ch_blacklist = Channel.empty()
     if (blacklist) {
         if (blacklist.endsWith('.gz')) {
-            ch_blacklist = GUNZIP_BLACKLIST ( [ [:], blacklist ] ).gunzip.map{ it[1] }
+            ch_blacklist = GUNZIP_BLACKLIST([[:], blacklist]).gunzip.map { it[1] }
             ch_versions  = ch_versions.mix(GUNZIP_BLACKLIST.out.versions)
         } else {
             ch_blacklist = Channel.value(file(blacklist))
@@ -99,17 +103,17 @@ workflow PREPARE_GENOME {
     if (!gene_bed) {
         make_bed = true
     } else if (genome && gtf) {
-        if (genomes[ genome ].gtf != gtf) {
+        if (genomes[genome].gtf != gtf) {
             make_bed = true
         }
     }
 
     if (make_bed) {
-        ch_gene_bed = GTF2BED ( ch_gtf ).bed
+        ch_gene_bed = GTF2BED(ch_gtf).bed
         ch_versions = ch_versions.mix(GTF2BED.out.versions)
     } else {
         if (gene_bed.endsWith('.gz')) {
-            ch_gene_bed = GUNZIP_GENE_BED ( [ [:], gene_bed ] ).gunzip.map{ it[1] }
+            ch_gene_bed = GUNZIP_GENE_BED([[:], gene_bed]).gunzip.map { it[1] }
             ch_versions = ch_versions.mix(GUNZIP_GENE_BED.out.versions)
         } else {
             ch_gene_bed = Channel.value(file(gene_bed))
@@ -119,22 +123,22 @@ workflow PREPARE_GENOME {
     //
     // Create chromosome sizes file
     //
-    CUSTOM_GETCHROMSIZES ( ch_fasta.map { [ [:], it ] } )
+    CUSTOM_GETCHROMSIZES(ch_fasta.map { [[:], it] })
     ch_chrom_sizes = CUSTOM_GETCHROMSIZES.out.sizes.map { it[1] }
-    ch_fai         = CUSTOM_GETCHROMSIZES.out.fai.map{ it[1] }
+    ch_fai         = CUSTOM_GETCHROMSIZES.out.fai.map { it[1] }
     ch_versions    = ch_versions.mix(CUSTOM_GETCHROMSIZES.out.versions)
 
     //
     // Prepare genome intervals for filtering by removing regions in blacklist file
     //
     ch_genome_filtered_bed = Channel.empty()
 
-    GENOME_BLACKLIST_REGIONS (
+    GENOME_BLACKLIST_REGIONS(
         ch_chrom_sizes,
         ch_blacklist.ifEmpty([])
     )
     ch_genome_filtered_bed = GENOME_BLACKLIST_REGIONS.out.bed
-    ch_versions = ch_versions.mix(GENOME_BLACKLIST_REGIONS.out.versions)
+    ch_versions            = ch_versions.mix(GENOME_BLACKLIST_REGIONS.out.versions)
 
     //
     // Uncompress BWA index or generate from scratch if required
@@ -143,13 +147,13 @@ workflow PREPARE_GENOME {
     if (prepare_tool_index == 'bwa') {
         if (bwa_index) {
             if (bwa_index.endsWith('.tar.gz')) {
-                ch_bwa_index = UNTAR_BWA_INDEX ( [ [:], bwa_index ] ).untar
+                ch_bwa_index = UNTAR_BWA_INDEX([[:], bwa_index]).untar
                 ch_versions  = ch_versions.mix(UNTAR_BWA_INDEX.out.versions)
             } else {
-                ch_bwa_index = [ [:], file(bwa_index) ]
+                ch_bwa_index = [[:], file(bwa_index)]
             }
         } else {
-            ch_bwa_index = BWA_INDEX ( ch_fasta.map { [ [:], it ] } ).index
+            ch_bwa_index = BWA_INDEX(ch_fasta.map { [[:], it] }).index
             ch_versions  = ch_versions.mix(BWA_INDEX.out.versions)
         }
     }
@@ -161,13 +165,13 @@ workflow PREPARE_GENOME {
     if (prepare_tool_index == 'bowtie2') {
         if (bowtie2_index) {
             if (bowtie2_index.endsWith('.tar.gz')) {
-                ch_bowtie2_index = UNTAR_BOWTIE2_INDEX ( [ [:], bowtie2_index ] ).untar
-                ch_versions  = ch_versions.mix(UNTAR_BOWTIE2_INDEX.out.versions)
+                ch_bowtie2_index = UNTAR_BOWTIE2_INDEX([[:], bowtie2_index]).untar
+                ch_versions      = ch_versions.mix(UNTAR_BOWTIE2_INDEX.out.versions)
             } else {
-                ch_bowtie2_index = [ [:], file(bowtie2_index) ]
+                ch_bowtie2_index = [[:], file(bowtie2_index)]
             }
         } else {
-            ch_bowtie2_index = BOWTIE2_BUILD ( ch_fasta.map { [ [:], it ] } ).index
+            ch_bowtie2_index = BOWTIE2_BUILD(ch_fasta.map { [[:], it] }).index
             ch_versions      = ch_versions.mix(BOWTIE2_BUILD.out.versions)
         }
     }
@@ -179,14 +183,14 @@ workflow PREPARE_GENOME {
     if (prepare_tool_index == 'chromap') {
         if (chromap_index) {
             if (chromap_index.endsWith('.tar.gz')) {
-                ch_chromap_index = UNTARFILES ( [ [:], chromap_index ] ).files
-                ch_versions  = ch_versions.mix(UNTARFILES.out.versions)
+                ch_chromap_index = UNTARFILES([[:], chromap_index]).files
+                ch_versions      = ch_versions.mix(UNTARFILES.out.versions)
             } else {
-                ch_chromap_index = [ [:], file(chromap_index) ]
+                ch_chromap_index = [[:], file(chromap_index)]
             }
         } else {
-            ch_chromap_index = CHROMAP_INDEX ( ch_fasta.map { [ [:], it ] } ).index
-            ch_versions  = ch_versions.mix(CHROMAP_INDEX.out.versions)
+            ch_chromap_index = CHROMAP_INDEX(ch_fasta.map { [[:], it] }).index
+            ch_versions      = ch_versions.mix(CHROMAP_INDEX.out.versions)
         }
     }
 
@@ -197,13 +201,13 @@ workflow PREPARE_GENOME {
     if (prepare_tool_index == 'star') {
         if (star_index) {
             if (star_index.endsWith('.tar.gz')) {
-                ch_star_index = UNTAR_STAR_INDEX ( [ [:], star_index ] ).untar.map{ it[1] }
+                ch_star_index = UNTAR_STAR_INDEX([[:], star_index]).untar.map { it[1] }
                 ch_versions   = ch_versions.mix(UNTAR_STAR_INDEX.out.versions)
             } else {
                 ch_star_index = Channel.value(file(star_index))
             }
         } else {
-            ch_star_index = STAR_GENOMEGENERATE ( ch_fasta, ch_gtf ).index
+            ch_star_index = STAR_GENOMEGENERATE(ch_fasta, ch_gtf).index
             ch_versions   = ch_versions.mix(STAR_GENOMEGENERATE.out.versions)
         }
     }
@@ -219,5 +223,5 @@ workflow PREPARE_GENOME {
     bowtie2_index = ch_bowtie2_index          //    path: bowtie2/index/
     chromap_index = ch_chromap_index          //    path: genome.index
     star_index    = ch_star_index             //    path: star/index/
-    versions    = ch_versions.ifEmpty(null)   // channel: [ versions.yml ]
+    versions      = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
 }