Spelling and channel names

modules/pigz.nf

@@ -3,7 +3,7 @@ A parallel implementation of gzip for modern
 multi-processor, multi-core machines
 https://zlib.net/pigz/
 */
-process fasta_uncompress {
+process fasta_unzip {
     tag "$genome"
     label 'pigz'
 

nextflow.config

@@ -16,7 +16,7 @@ params {
 }
 
 // Include a base config (2 forks of 1 CPU)
-includeConfig "$baseDir/config/ressources/base.config"
+includeConfig "$baseDir/config/resources/base.config"
 
 profiles {
 
@@ -32,7 +32,7 @@ profiles {
         params.sifPath = "${baseDir}/sif_images"
         // singularity.envWhitelist = '' // Comma separated list of environment variable names to be included in the container environment.	
         includeConfig "$baseDir/config/softwares.config"
-        includeConfig "$baseDir/config/ressources/hpc.config"
+        includeConfig "$baseDir/config/resources/hpc.config"
     }
 
     debug { process.beforeScript = 'env' }
@@ -50,10 +50,10 @@ profiles {
         includeConfig "$baseDir/config/softwares.config"
     }
     local {
-        includeConfig "$baseDir/config/ressources/local.config"
+        includeConfig "$baseDir/config/resources/local.config"
     }
     test {
-        params.aline_profiles = "${baseDir}/config/ressources/base_aline.config" 
+        params.aline_profiles = "${baseDir}/config/resources/base_aline.config" 
         params.aligner        = "STAR" 
         params.reads          = "${baseDir}/data/chr21/chr21_small_R1.fastq.gz "
         params.genome         = "${baseDir}/data/chr21/chr21_small.fasta.gz"
@@ -62,7 +62,7 @@ profiles {
         params.read_type      = "short_single"
     }
     test2 {
-        params.aline_profiles = "${baseDir}/config/ressources/base_aline.config" 
+        params.aline_profiles = "${baseDir}/config/resources/base_aline.config" 
         params.aligner        = "STAR" 
         params.reads          = "${baseDir}/data/chr21/"
         params.genome         = "${baseDir}/data/chr21/chr21_small.fasta.gz" 

rain.nf

@@ -36,7 +36,7 @@ params.aggregation_mode = "all"
 aline_profile_allowed = [ 'docker', 'singularity', 'local', 'itrop' ]
 
 // Aline ressource config used
-params.aline_profiles = "$baseDir/config/ressources/custom_aline.config" // e.g. "docker, singularity,itrop,local"
+params.aline_profiles = "$baseDir/config/resources/custom_aline.config" // e.g. "docker, singularity,itrop,local"
 
 // Aligner params
 align_tools = ['hisat2', "STAR"]
@@ -139,7 +139,7 @@ include {fastp} from './modules/fastp.nf'
 include {fastqc as fastqc_raw; fastqc as fastqc_ali; fastqc as fastqc_dup; fastqc as fastqc_clip} from './modules/fastqc.nf'
 include {gatk_markduplicates } from './modules/gatk.nf'
 include {multiqc} from './modules/multiqc.nf'
-include {fasta_uncompress} from "$baseDir/modules/pigz.nf"
+include {fasta_unzip} from "$baseDir/modules/pigz.nf"
 include {samtools_index; samtools_fasta_index; samtools_sort_bam} from './modules/samtools.nf'
 include {reditools2} from "./modules/reditools2.nf"
 include {reditools3} from "./modules/reditools3.nf"
@@ -205,16 +205,16 @@ workflow {
         Channel.fromPath(params.genome, checkIfExists: true)
                .ifEmpty { exit 1, "Cannot find genome matching ${params.genome}!\n" }
                .set{genome_raw}
-        // uncompress it if needed
-        fasta_uncompress(genome_raw)
-        fasta_uncompress.out.genomeFa.set{genome_ch} // set genome to the output of fasta_uncompress
+        // unzip it if needed
+        fasta_unzip(genome_raw)
+        fasta_unzip.out.genomeFa.set{genome} // set genome to the output of fasta_unzip
 // ----------------------------------------------------------------------------
         // --- DEAL WITH ANNOTATION ---
-        Channel.empty().set{annotation_ch}
+        Channel.empty().set{annotation}
         if (params.annotation){
         Channel.fromPath(params.annotation, checkIfExists: true)
                .ifEmpty { exit 1, "Cannot find annotation matching ${params.annotation}!\n" }
-               .set{annotation_ch}
+               .set{annotation}
         }
 // ----------------------------------------------------------------------------
         def path_csv = params.csv
@@ -368,7 +368,7 @@ workflow {
                 "${workflow.resume?'-resume':''} -profile ${aline_profile}", // workflow opts supplied as params for flexibility
                 "-config ${params.aline_profiles}",
                 "--reads ${path_reads}",
-                genome_ch,
+                genome,
                 "--read_type ${params.read_type}",
                 "--aligner ${params.aligner}",
                 "--library_type ${params.library_type}",
@@ -390,7 +390,7 @@ workflow {
             if (params.library_type.contains("auto") ) {
                 log.info "Library type is set to auto, extracting it from salmon output"
                 // GET TUPLE [ID, OUTPUT_SALMON_LIBTYPE] FILES
-                ALIGNMENT.out.output
+                aline_alignments_all = ALIGNMENT.out.output
                     .map { dir ->
                         files("$dir/salmon_libtype/*/*.json", checkIfExists: true)  // Find BAM files inside the output directory
                     }
@@ -404,7 +404,7 @@ workflow {
                 aline_libtype = extract_libtype(aline_libtype)
                 aline_alignments.join(aline_libtype)
                     .map { key, val1, val2 -> tuple(key, val1, val2) }
-                    .set { aline_alignments_all }
+
             } else {
                 log.info "Library type is set to ${params.library_type}, no need to extract it from salmon output"
                 aline_alignments_all = aline_alignments.map { name, bam -> tuple(name, bam, params.library_type) }
@@ -418,20 +418,8 @@ workflow {
         }
 
         // call rain
-        all_bams = aline_alignments_all.mix(sorted_bam)
+        tuple_sample_sortedbam = aline_alignments_all.mix(sorted_bam)
         log.info "The following bam file(s) will be processed by RAIN:"
-        all_bams.view()
-        rain(all_bams, genome_ch, annotation_ch)
-}
-
-workflow rain {
-
-    take:
-        tuple_sample_sortedbam
-        genome
-        annnotation
-
-    main:
 
         // STEP 1 QC with fastp ?
         Channel.empty().set{logs}
@@ -459,30 +447,31 @@ workflow rain {
         samtools_index(tuple_sample_bam_processed)
         // report with multiqc
         // multiqc(logs.collect(),params.multiqc_config)
-        // Create a fasta index file of the reference genome
-        samtools_fasta_index(genome.collect())
-
-        normalize_gxf(annnotation)
 
         // Select site detection tool
         switch (params.edit_site_tool) {
             case "jacusa2":
+                // Create a fasta index file of the reference genome
+                samtools_fasta_index(genome.collect())
                 jacusa2(samtools_index.out.tuple_sample_bam_bamindex, samtools_fasta_index.out.tuple_fasta_fastaindex.collect())
                 break
             case "sapin":
                 sapin(tuple_sample_bam_processed, genome.collect())
                 break
             case "reditools2":
                 reditools2(samtools_index.out.tuple_sample_bam_bamindex, genome.collect(), params.region)
+                normalize_gxf(annotation.collect())
                 pluviometer(reditools2.out.tuple_sample_serial_table, normalize_gxf.out.gff.collect(), "reditools2")
                 break
             case "reditools3":
                 reditools3(samtools_index.out.tuple_sample_bam_bamindex, genome.collect())
+                normalize_gxf(annotation.collect())
                 pluviometer(reditools3.out.tuple_sample_serial_table, normalize_gxf.out.gff.collect(), "reditools3")
                 break
             default:
                 exit(1, "Wrong edit site tool was passed")
         }
+
 }