Fix ref genomes & other behaviour

CHANGELOG.md

@@ -15,7 +15,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Fixed`
 * [#172](https://github.com/nf-core/eager/pull/152) - DamageProfiler errors [won't crash entire pipeline anymore](https://github.com/nf-core/eager/issues/171)
-* [#174](https://github.com/nf-core/eager/pull/190) - Publish DeDup files [properly](https://github.com/nf-core/eager/issues/183) 
+* [#174](https://github.com/nf-core/eager/pull/190) - Publish DeDup files [properly](https://github.com/nf-core/eager/issues/183)
+* TBF - Fix reference [issues](https://github.com/nf-core/eager/issues/150)
 
 ### `Dependencies`
 

main.nf

@@ -226,36 +226,30 @@ params.strip_input_fastq = false
 params.strip_mode = 'strip'
 
 
-ch_multiqc_config = Channel.fromPath(params.multiqc_config)
-ch_output_docs = Channel.fromPath("$baseDir/docs/output.md")
-Channel.fromPath("$baseDir/assets/where_are_my_files.txt")
-       .into{ ch_where_for_bwa_index; ch_where_for_fasta_index; ch_where_for_seqdict}
-
+multiqc_config = file(params.multiqc_config)
+output_docs = file("$baseDir/docs/output.md")
+where_are_my_files = file("$baseDir/assets/where_are_my_files.txt")
 // Validate inputs
 if("${params.fasta}".endsWith(".gz")){
     //Put the zip into a channel, then unzip it and forward to downstream processes. DONT unzip in all steps, this is inefficient as NXF links the files anyways from work to work dir
-    Channel.fromPath("${params.fasta}")
-            .ifEmpty { exit 1, "No genome specified! Please specify one with --fasta"}
-            .set {ch_unzip_fasta}
+    zipped_fasta = file("${params.fasta}")
 
     process unzip_reference{
         tag "$zipfasta"
 
         input:
-        file zipfasta from ch_unzip_fasta
+        file zipped_fasta
 
         output:
-        file "*.fasta" into (ch_fasta_for_bwa_indexing, ch_fasta_for_faidx_indexing, ch_fasta_for_dict_indexing,  ch_fasta_for_damageprofiler, ch_fasta_for_qualimap, ch_fasta_for_pmdtools, ch_fasta_for_circularmapper_index)
+        file "*.fasta" into fasta_for_indexing
 
         script:
         """
         pigz -f -d -p ${task.cpus} $zipfasta
         """
     }   
     } else {
-    Channel.fromPath("${params.fasta}")
-    .ifEmpty { exit 1, "No genome specified! Please specify one with --fasta"}
-    .into {ch_fasta_for_bwa_indexing;ch_fasta_for_faidx_indexing;ch_fasta_for_dict_indexing; ch_fasta_for_damageprofiler; ch_fasta_for_qualimap; ch_fasta_for_pmdtools; ch_fasta_for_circularmapper_index}
+    fasta_for_indexing = file("${params.fasta}")
 }
 
 //Index files provided? Then check whether they are correct and complete
@@ -280,12 +274,6 @@ if (params.skip_collapse  && params.singleEnd){
     exit 1, "--skip_collapse can only be set for pairedEnd samples!"
 }
 
-//AWSBatch sanity checking
-if(workflow.profile == 'awsbatch'){
-    if (!params.awsqueue || !params.awsregion) exit 1, "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
-    if (!workflow.workDir.startsWith('s3') || !params.outdir.startsWith('s3')) exit 1, "Specify S3 URLs for workDir and outdir parameters on AWSBatch!"
-}
-
 //Strip mode sanity checking
 if (params.strip_input_fastq){
     if (!(['strip','replace'].contains(params.strip_mode))) {
@@ -311,11 +299,6 @@ if( workflow.profile == 'awsbatch') {
   // Prevent trace files to be stored on S3 since S3 does not support rolling files.
   if (workflow.tracedir.startsWith('s3:')) exit 1, "Specify a local tracedir or run without trace! S3 cannot be used for tracefiles."
 }
-
-// Stage config files
-ch_multiqc_config = Channel.fromPath(params.multiqc_config)
-ch_output_docs = Channel.fromPath("$baseDir/docs/output.md")
-
 /*
  * Create a channel for input read files
  * Dump can be used for debugging purposes, e.g. using the -dump-channels operator on run
@@ -458,8 +441,8 @@ process makeBWAIndex {
     when: !params.bwa_index && params.fasta && (params.aligner == 'bwa' || params.bwamem)
 
     input:
-    file fasta from ch_fasta_for_bwa_indexing
-    file wherearemyfiles from ch_where_for_bwa_index
+    file fasta from fasta_for_indexing
+    file where_are_my_files
 
     output:
     file "bwa_index" into (ch_bwa_index,ch_bwa_index_bwamem)
@@ -491,8 +474,8 @@ process makeFastaIndex {
     when: !params.fasta_index && params.fasta && params.aligner == 'bwa'
 
     input:
-    file fasta from ch_fasta_for_faidx_indexing
-    file wherearemyfiles from ch_where_for_fasta_index
+    file fasta from fasta_for_indexing
+    file where_are_my_files
 
     output:
     file "faidx/${base}.fasta.fai" into ch_fasta_faidx_index
@@ -525,8 +508,8 @@ process makeSeqDict {
     when: !params.seq_dict && params.fasta
 
     input:
-    file fasta from ch_fasta_for_dict_indexing
-    file wherearemyfiles from ch_where_for_seqdict
+    file fasta from fasta_for_indexing
+    file where_are_my_files
 
     output:
     file "seq_dict/*.dict" into ch_seq_dict
@@ -723,7 +706,7 @@ process bwa {
     input:
     set val(name), file(reads) from ch_clipped_reads.mix(ch_read_files_converted_mapping_bwa)
 
-    file index from ch_bwa_index.first()
+    file index from ch_bwa_index
 
 
     output:
@@ -767,7 +750,7 @@ process circulargenerator{
     when: params.circularmapper
 
     input:
-    file fasta from ch_fasta_for_circularmapper_index
+    file fasta from fasta_for_indexing
 
     output:
     file "cm_index" into ch_circularmapper_indices
@@ -793,7 +776,7 @@ process circularmapper{
 
     input:
     set val(name), file(reads) from ch_clipped_reads_circularmapper.mix(ch_read_files_converted_mapping_cm)
-    file index from ch_circularmapper_indices.first()
+    file index from ch_circularmapper_indices
 
     output:
     file "*.sorted.bam" into ch_mapped_reads_idxstats_cm,ch_mapped_reads_filter_cm,ch_mapped_reads_preseq_cm, ch_mapped_reads_damageprofiler_cm, ch_circular_mapped_reads_strip
@@ -836,7 +819,7 @@ process bwamem {
 
     input:
     set val(name), file(reads) from ch_clipped_reads_bwamem.mix(ch_read_files_converted_mapping_bwamem)
-    file index from ch_bwa_index_bwamem.first()
+    file index from ch_bwa_index_bwamem
 
     output:
     file "*.sorted.bam" into ch_bwamem_mapped_reads_idxstats,ch_bwamem_mapped_reads_filter,ch_bwamem_mapped_reads_preseq, ch_bwamem_mapped_reads_damageprofiler, ch_bwamem_mapped_reads_strip
@@ -1061,7 +1044,7 @@ process damageprofiler {
 
     input:
     file bam from ch_mapped_reads_damageprofiler.mix(ch_mapped_reads_damageprofiler_cm,ch_bwamem_mapped_reads_damageprofiler)
-    file fasta from ch_fasta_for_damageprofiler.first()
+    file fasta from fasta_for_indexing
     file bai from ch_bam_index_for_damageprofiler
 
 
@@ -1088,7 +1071,7 @@ process qualimap {
 
     input:
     file bam from ch_bam_filtered_qualimap
-    file fasta from ch_fasta_for_qualimap.first()
+    file fasta from fasta_for_indexing
 
     output:
     file "*" into ch_qualimap_results
@@ -1152,7 +1135,7 @@ process pmdtools {
 
     input: 
     file bam from ch_for_pmdtools
-    file fasta from ch_fasta_for_pmdtools
+    file fasta from fasta_for_indexing
 
     output:
     file "*.bam" into ch_bam_after_pmdfiltering
@@ -1237,7 +1220,7 @@ process output_documentation {
     publishDir "${params.outdir}/Documentation", mode: 'copy'
 
     input:
-    file output_docs from ch_output_docs
+    file output_docs
 
     output:
     file "results_description.html"
@@ -1291,7 +1274,7 @@ process multiqc {
     publishDir "${params.outdir}/MultiQC", mode: 'copy'
 
     input:
-    file multiqc_config from ch_multiqc_config.collect().ifEmpty([])
+    file multiqc_config
     file ('fastqc_raw/*') from ch_fastqc_results.collect().ifEmpty([])
     file('fastqc/*') from ch_fastqc_after_clipping.collect().ifEmpty([])
     file ('software_versions/software_versions_mqc*') from software_versions_yaml.collect().ifEmpty([])