Merge pull request #38 from hoelzer/dev

Dev
rki-mf1 · Jun 23, 2021 · 011481d · 011481d
2 parents 96520f2 + 5b8f1a5
commit 011481d
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Showing 3 changed files with 29 additions and 29 deletions.
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,12 +1,13 @@
 custom_data:
     mapping:
         file_format: 'tsv'
-        section_name: 'Mapping statistics'
-        anchor: 'mapping'
+        section_name: 'Contamination statistics'
+        description: "Mapped and unmapped reads (or contigs) for the mapping result against the contamination. Short and sweet: mapped = contamination."
+        anchor: 'contamination'
         plot_type: 'bargraph'
         pconfig:
-            id: 'Mapping'
-            title: 'Mapping statistics'
+            id: 'Contamination'
+            title: 'Contamination statistics'
 
 sp:
     quast:

diff --git a/clean.nf b/clean.nf
@@ -177,7 +177,7 @@ include { download_host; check_own; concat_contamination } from './modules/get_h
 include { minimap2_fasta; minimap2_nano; minimap2_illumina } from './modules/minimap2'
 include { bbduk } from './modules/bbmap'
 
-include { rename_reads; restore_reads; get_number_of_reads; minimap2Stats; bbdukStats; writeLog } from './modules/utils'
+include { compress_reads; get_number_of_reads; minimap2Stats; bbdukStats; writeLog } from './modules/utils'
 
 include { fastqc; nanoplot; format_nanoplot_report; quast; multiqc } from './modules/qc'
 
@@ -272,16 +272,16 @@ workflow clean_nano {
         .mix(rRNAChannel).collect()
       concat_contamination( nano_input_ch.map{ it -> it[0] }, 'minimap2', contamination )
     }
-    rename_reads(nano_input_ch, 'single')
-    minimap2_nano(rename_reads.out, concat_contamination.out.fa)
+    // rename_reads(nano_input_ch, 'single')
+    minimap2_nano(nano_input_ch, concat_contamination.out.fa)
     writeLog(nano_input_ch.map{ it -> it[0] }, 'minimap2', nano_input_ch.map{ it -> it[1] }, contamination)
-    get_number_of_reads(rename_reads.out, 'single')
+    get_number_of_reads(nano_input_ch, 'single')
     minimap2Stats(minimap2_nano.out.idxstats.join(get_number_of_reads.out))
-    restore_reads(minimap2_nano.out.cleaned_reads.concat(minimap2_nano.out.contaminated_reads), 'single', 'minimap2')
+    compress_reads(minimap2_nano.out.cleaned_reads.concat(minimap2_nano.out.contaminated_reads), 'single', 'minimap2')
   emit:
     stats = minimap2Stats.out.tsv
     in = nano_input_ch.map{ it -> it.plus(1, 'all') }
-    out = restore_reads.out
+    out = compress_reads.out
 } 
 
 workflow clean_illumina {
@@ -306,25 +306,25 @@ workflow clean_illumina {
         .mix(rRNAChannel).collect()
       concat_contamination( illumina_input_ch.map{ it -> it[0] }, params.bbduk ? 'bbduk' : 'minimap2', contamination )
     }
-    rename_reads(illumina_input_ch, 'paired')
+    // rename_reads(illumina_input_ch, 'paired')
     if (params.bbduk){
-      bbduk(rename_reads.out, concat_contamination.out.fa, 'paired')
+      bbduk(illumina_input_ch, concat_contamination.out.fa, 'paired')
       writeLog(illumina_input_ch.map{ it -> it[0] }, 'bbduk', illumina_input_ch.map{ it -> it[1] }, contamination)
       bbdukStats(bbduk.out.stats)
-      restore_reads(bbduk.out.cleaned_reads.concat(bbduk.out.contaminated_reads), 'paired', 'bbduk')
+      compress_reads(bbduk.out.cleaned_reads.concat(bbduk.out.contaminated_reads), 'paired', 'bbduk')
       stats = bbdukStats.out.tsv
     } else {
-      minimap2_illumina(rename_reads.out, concat_contamination.out.fa, 'paired')
+      minimap2_illumina(illumina_input_ch, concat_contamination.out.fa, 'paired')
       writeLog(illumina_input_ch.map{ it -> it[0] }, 'minimap2', illumina_input_ch.map{ it -> it[1] }, contamination)
-      get_number_of_reads(rename_reads.out, 'paired')
+      get_number_of_reads(illumina_input_ch, 'paired')
       minimap2Stats(minimap2_illumina.out.idxstats.join(get_number_of_reads.out))
-      restore_reads(minimap2_illumina.out.cleaned_reads.concat(minimap2_illumina.out.contaminated_reads), 'paired', 'minimap2')
+      compress_reads(minimap2_illumina.out.cleaned_reads.concat(minimap2_illumina.out.contaminated_reads), 'paired', 'minimap2')
       stats = minimap2Stats.out.tsv
     }
   emit:
     stats = stats
     in = illumina_input_ch.map{ it -> it.plus(1, 'all') }
-    out = restore_reads.out
+    out = compress_reads.out
 } 
 
 workflow clean_illumina_single {
@@ -349,25 +349,25 @@ workflow clean_illumina_single {
         .mix(rRNAChannel).collect()
       concat_contamination( illumina_single_end_input_ch.map{ it -> it[0] }, params.bbduk ? 'bbduk' : 'minimap2', contamination )
     }
-    rename_reads(illumina_single_end_input_ch, 'single')
+    // rename_reads(illumina_single_end_input_ch, 'single')
     if (params.bbduk){
-      bbduk(rename_reads.out, concat_contamination.out.fa, 'single')
+      bbduk(illumina_single_end_input_ch, concat_contamination.out.fa, 'single')
       writeLog(illumina_single_end_input_ch.map{ it -> it[0] }, 'bbduk', illumina_single_end_input_ch.map{ it -> it[1] }, contamination)
       bbdukStats(bbduk.out.stats)
       stats = bbdukStats.out.tsv
-      restore_reads(bbduk.out.cleaned_reads.concat(bbduk.out.contaminated_reads), 'single', 'bbduk')
+      compress_reads(bbduk.out.cleaned_reads.concat(bbduk.out.contaminated_reads), 'single', 'bbduk')
     } else {
-      minimap2_illumina(rename_reads.out, concat_contamination.out.fa, 'single')
+      minimap2_illumina(illumina_single_end_input_ch, concat_contamination.out.fa, 'single')
       writeLog(illumina_single_end_input_ch.map{ it -> it[0] }, 'minimap2', illumina_single_end_input_ch.map{ it -> it[1] }, contamination)
-      get_number_of_reads(rename_reads.out, 'single')
+      get_number_of_reads(illumina_single_end_input_ch, 'single')
       minimap2Stats(minimap2_illumina.out.idxstats.join(get_number_of_reads.out))
       stats = minimap2Stats.out.tsv
-      restore_reads(minimap2_illumina.out.cleaned_reads.concat(minimap2_illumina.out.contaminated_reads), 'single', 'minimap2')
+      compress_reads(minimap2_illumina.out.cleaned_reads.concat(minimap2_illumina.out.contaminated_reads), 'single', 'minimap2')
     }
     emit:
       stats = stats
       in = illumina_single_end_input_ch.map{ it -> it.plus(1, 'all') }
-      out = restore_reads.out
+      out = compress_reads.out
 } 
 
 workflow qc_fasta {

diff --git a/modules/utils.nf b/modules/utils.nf
@@ -47,7 +47,7 @@ process rename_reads {
   }
 }
 
-process restore_reads {
+process compress_reads {
   label 'basics'
 
   publishDir "${params.output}/${name}/${tool}", mode: 'copy', pattern: "*.gz"
@@ -63,13 +63,12 @@ process restore_reads {
   script:
   if ( mode == 'paired' ) {
     """
-    # restore the original read IDs
-    sed 's/DECONTAMINATE/ /g' ${reads}[0] | awk 'BEGIN{LINE=0};{if(LINE % 4 == 0 || LINE == 0){print \$0"/1"}else{print \$0};LINE++;}' | pigz -p ${task.cpus} > ${name}_1.${type}.fastq.gz 
-    sed 's/DECONTAMINATE/ /g' ${reads}[1] | awk 'BEGIN{LINE=0};{if(LINE % 4 == 0 || LINE == 0){print \$0"/2"}else{print \$0};LINE++;}' | pigz -p ${task.cpus} > ${name}_2.${type}.fastq.gz
+    pigz -fc -p ${task.cpus} ${reads[0]} > ${name}_1.${type}.fastq.gz 
+    pigz -fc -p ${task.cpus} ${reads[1]} > ${name}_2.${type}.fastq.gz
     """
   } else {
     """
-    sed 's/DECONTAMINATE/ /g' ${reads} | pigz -p ${task.cpus} > ${name}.${type}.fastq.gz
+    pigz -fc -p ${task.cpus} ${reads} > ${name}.${type}.fastq.gz
     """
   }
 }