Merge develop with release branch v0.5.0

Fastp/0.14.1/Fastp.nf

@@ -13,7 +13,7 @@ process Fastp {
 
     script:
         //adapted from https://github.com/nf-core/eager/blob/master/LICENSE, Copyright (c) Alexander Peltzer, Stephen Clayton, James A. Fellows Yates, Maxime Borry
-        if (params.singleEnd) {
+        if (params.single_end) {
             """
             fastp --in1 ${fastq_files[0]} --out1 "${fastq_files[0].simpleName}.trim.fastq.gz" -j ${sample_id}_fastp.json ${params.optional}
             """

Fastp/0.20.1/Fastp.nf

@@ -13,7 +13,7 @@ process Fastp {
 
     script:
         //adapted from https://github.com/nf-core/eager/blob/master/LICENSE, Copyright (c) Alexander Peltzer, Stephen Clayton, James A. Fellows Yates, Maxime Borry
-        if (params.singleEnd) {
+        if (params.single_end) {
             """
             fastp --in1 ${fastq_files[0]} --out1 "${fastq_files[0].simpleName}_trim.fastq.gz" -j ${sample_id}_fastp.json ${params.optional}
             """

Pandocker/21.02/MarkdownToPdf.nf

@@ -0,0 +1,24 @@
+process MarkdownToPdf {
+    tag {"Pandocker MarkdownToPdf"}
+    label 'Pandocker_21_02'
+    label 'Pandocker_21_02_MarkdownToPdf'
+
+    container = 'library://dalibo/pandocker:v21.02'
+    shell = ['/bin/bash', '-euo', 'pipefail']
+
+    input:        
+        path(md_file)
+
+    output:        
+        path("${md_file.baseName}.pdf")
+
+    script:
+        """
+        pandoc ${md_file} \
+            --variable urlcolor=blue \
+            -s \
+            --toc \
+            -f markdown \
+            -o ${md_file.baseName}.pdf
+        """
+}

STARFusion/1.8.1/STARFusion.nf

@@ -17,7 +17,7 @@ process STARFusion {
     script:
         //Adapted code from: https://github.com/nf-core/rnafusion - MIT License - Copyright (c) Martin Proks
         def avail_mem = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
-        def read_args = params.singleEnd ? "--left_fq ${fastq_files[0]}" : "--left_fq ${fastq_files[0]} --right_fq ${fastq_files[1]}"
+        def read_args = params.single_end ? "--left_fq ${fastq_files[0]}" : "--left_fq ${fastq_files[0]} --right_fq ${fastq_files[1]}"
         """
         STAR \
             --genomeDir ${star_index} \

Salmon/1.2.1/Quant.nf

@@ -14,13 +14,13 @@ process Quant {
 
     script:
         //Adapted code from: https://github.com/nf-core/rnaseq - MIT License - Copyright (c) Phil Ewels, Rickard Hammarén
-        def rnastrandness = params.singleEnd ? 'U' : 'IU'
+        def rnastrandness = params.single_end ? 'U' : 'IU'
         if (params.stranded && !params.unstranded) {
-            rnastrandness = params.singleEnd ? 'SF' : 'ISF'
+            rnastrandness = params.single_end ? 'SF' : 'ISF'
         } else if (params.revstranded && !params.unstranded) {
-            rnastrandness = params.singleEnd ? 'SR' : 'ISR'
+            rnastrandness = params.single_end ? 'SR' : 'ISR'
         }
-        def endedness = params.singleEnd ? "-r ${fastq_files[0]}" : "-1 ${fastq_files[0]} -2 ${fastq_files[1]}"
+        def endedness = params.single_end ? "-r ${fastq_files[0]}" : "-1 ${fastq_files[0]} -2 ${fastq_files[1]}"
         def unmapped = params.saveUnaligned ? "--writeUnmappedNames" : ''
 
         """

SortMeRNA/4.2.0/SortMeRNA.nf

@@ -17,7 +17,7 @@ process SortMeRNA {
     script:
         def Refs =  db_fasta.collect{ "$it" }.join(" -ref ")
         def report_title = fastq_files[0].simpleName.split("_R1_")[0]  
-        if (params.singleEnd) {
+        if (params.single_end) {
             """
             sortmerna -ref ${Refs} \
                 -reads ${fastq_files} \
@@ -31,6 +31,8 @@ process SortMeRNA {
             gzip -f < non-rRNA-reads.fastq > ${fastq_files[0].simpleName}_non_rRNA.fastq.gz
             gzip -f < rRNA-reads.fastq > ${fastq_files[0].simpleName}_filtered_rRNA.fastq.gz
             mv rRNA-reads.log ${report_title}_rRNA_report.txt
+            rm non-rRNA-reads.fastq
+            rm rRNA-reads.fastq
             """
         } else {
             """
@@ -49,6 +51,10 @@ process SortMeRNA {
             gzip < rRNA-reads_fwd.fastq >  ${fastq_files[0].simpleName}_filtered_rRNA.fastq.gz
             gzip < rRNA-reads_rev.fastq >  ${fastq_files[1].simpleName}_filtered_rRNA.fastq.gz
             mv rRNA-reads.log ${report_title}_rRNA_report.txt
+            rm non-rRNA-reads_fwd.fastq
+            rm non-rRNA-reads_rev.fastq
+            rm rRNA-reads_fwd.fastq
+            rm rRNA-reads_rev.fastq
             """
         }
 }

SortMeRNA/4.3.3/SortMeRNA.nf

@@ -0,0 +1,55 @@
+process SortMeRNA {
+    tag {"SortMeRNA ${sample_id}"}
+    label 'SortMeRNA_4_3_3'
+    container = 'quay.io/biocontainers/sortmerna:4.3.3--h9ee0642_0'
+    shell = ['/bin/bash', '-euo', 'pipefail']
+
+    input:
+        tuple(sample_id, rg_id, path(fastq_files))
+        path(db_fasta) 
+
+    output:
+        tuple(sample_id, rg_id, path("*_non_rRNA.fastq.gz"), emit: non_rRNA_fastqs)
+        path("*_filtered_rRNA.fastq.gz", emit: rRNA_fastqs)
+        path("*_rRNA_report.txt", emit: qc_report)
+
+    script:
+        def refs =  db_fasta.collect{ "$it" }.join(" -ref ")
+        def report_title = fastq_files[0].simpleName.split("_R1_")[0]  
+        if (params.single_end) {
+            """
+            sortmerna -ref ${refs} \
+                -reads ${fastq_files} \
+                --num_alignments 1 \
+                --threads ${task.cpus} \
+                --fastx \
+                -workdir \${PWD} \
+                --aligned rRNA-reads \
+                --other non-rRNA-reads  \
+                --zip-out
+
+            mv non-rRNA-reads.fq.gz ${fastq_files[0].simpleName}_non_rRNA.fastq.gz
+            mv rRNA-reads.fq.gz ${fastq_files[0].simpleName}_filtered_rRNA.fastq.gz
+            mv rRNA-reads.log ${report_title}_rRNA_report.txt
+            """
+        } else {
+            """
+            sortmerna -ref ${refs} \
+                -reads ${fastq_files[0]} -reads ${fastq_files[1]} \
+                --num_alignments 1 \
+                --threads ${task.cpus} \
+                -workdir \${PWD} \
+                --fastx -paired_in \
+                --aligned rRNA-reads \
+                --other non-rRNA-reads \
+                -out2 \
+                --zip-out
+
+            mv non-rRNA-reads_fwd.fq.gz  ${fastq_files[0].simpleName}_non_rRNA.fastq.gz
+            mv non-rRNA-reads_rev.fq.gz  ${fastq_files[1].simpleName}_non_rRNA.fastq.gz
+            mv rRNA-reads_fwd.fq.gz  ${fastq_files[0].simpleName}_filtered_rRNA.fastq.gz
+            mv rRNA-reads_rev.fq.gz  ${fastq_files[1].simpleName}_filtered_rRNA.fastq.gz            
+            mv rRNA-reads.log ${report_title}_rRNA_report.txt
+            """
+        }
+}

Subread/2.0.0/FeatureCounts.nf

@@ -21,7 +21,7 @@ process FeatureCounts {
         def bam_list = bam_file.collect{ "$it" }.join(" ")
         def biotype = params.gencode ? "gene_type" : params.fc_group_features_type
         def extraAttributes = params.fc_extra_attributes ? "--extraAttributes ${params.fc_extra_attributes}" : ''
-        def fragment_mode = !params.singleEnd ? "-p": ''
+        def fragment_mode = !params.single_end ? "-p": ''
         //Get strandedness
         def featureCounts_direction = 0
         if (params.stranded && !params.unstranded) {

TrimGalore/0.6.5/TrimGalore.nf

@@ -13,7 +13,7 @@ process TrimGalore {
         path("*_fastqc.{zip,html}", optional: true, emit: fastqc_report) 
 
     script:
-        if (params.singleEnd) {
+        if (params.single_end) {
             """
             trim_galore ${fastq_files} --gzip ${params.optional}
             mv ${fastq_files[0].simpleName}_trimmed.fq.gz ${fastq_files[0].simpleName}_trimmed.fastq.gz 

Utils/MergeFastqLanes.nf

@@ -14,7 +14,7 @@ process MergeFastqLanes {
         barcode = rg_id.split('_')[1]
         def R1_pattern="${sample_id}_*_S*_L00*_R1_001*.fastq.gz"
         def R2_pattern="${sample_id}_*_S*_L00*_R2_001*.fastq.gz"
-        if (params.singleEnd) {
+        if (params.single_end) {
             """
             cat \$( ls ${R1_pattern} | sort | paste \$(printf "%0.s- " \$(seq 1 \$( ls ${R1_pattern} | wc -l)))) > ${sample_id}_${barcode}_merged_R1.fastq.gz
             """

Utils/workflow.nf

@@ -0,0 +1,16 @@
+process ExportParams {
+    tag {"Workflow Export Params"}
+    label 'Workflow_Export_Params'
+    shell = ['/bin/bash', '-euo', 'pipefail']
+    cache = false  //Disable cache to force a new export when restarting the workflow.
+
+    output:
+        path("workflow_params.txt")
+
+    script:
+        def workflow_params = params.collect{param -> "$param.key\t$param.value"}.sort().join("\n")
+        """
+        echo -e "param\tvalue" > workflow_params.txt
+        echo -e "${workflow_params}" >> workflow_params.txt
+        """
+}