Merge pull request #128 from nf-core/fastp-patch-removal

use proper working FASTP module

modules.json

@@ -43,8 +43,7 @@
                 },
                 "fastp": {
                     "branch": "master",
-                    "git_sha": "7e8ad566883449e7939062b5e2bcf53fc1e0002f",
+                    "git_sha": "2c70c1c1951aaf884d2e8d8d9c871db79f7b35aa"
-                    "patch": "modules/nf-core/modules/fastp/fastp.diff"
                 },
                 "fastqc": {
                     "branch": "master",

modules/nf-core/modules/fastp/fastp.diff

@@ -1,33 +0,0 @@
-Changes in module 'nf-core/modules/fastp'
---- modules/nf-core/modules/fastp/main.nf
-+++ modules/nf-core/modules/fastp/main.nf
-@@ -33,9 +33,8 @@
-         def fail_fastq = save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : ''
-         """
-         [ ! -f  ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz
--        cat ${prefix}.fastq.gz \\
--        | fastp \\
--            --stdin \\
-+        
-+        fastp \\
-             --stdout \\
-             --in1 ${prefix}.fastq.gz \\
-             --thread $task.cpus \\
-@@ -45,6 +44,7 @@
-             $args \\
-             2> ${prefix}.fastp.log \\
-         | gzip -c > ${prefix}.fastp.fastq.gz
-+
-         cat <<-END_VERSIONS > versions.yml
-         "${task.process}":
-             fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
-@@ -69,6 +69,7 @@
-             --detect_adapter_for_pe \\
-             $args \\
-             2> ${prefix}.fastp.log
-+            
- 
-         cat <<-END_VERSIONS > versions.yml
-         "${task.process}":
-
-************************************************************

modules/nf-core/modules/fastp/main.nf

@@ -26,14 +26,14 @@ process FASTP {
 
     script:
     def args = task.ext.args ?: ''
-    // Added soft-links to original fastqs for consistent naming in MultiQC
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def fail_fastq = save_trimmed_fail && meta.single_end ? "--failed_out ${prefix}.fail.fastq.gz" : save_trimmed_fail && !meta.single_end ? "--unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : ''
+    // Added soft-links to original fastqs for consistent naming in MultiQC
     // Use single ended for interleaved. Add --interleaved_in in config.
-    if (meta.single_end) {
+    if ( task.ext.args?.contains('--interleaved_in') ) {
-        def fail_fastq = save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : ''
         """
         [ ! -f  ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz
-        
+
         fastp \\
             --stdout \\
             --in1 ${prefix}.fastq.gz \\
@@ -45,13 +45,32 @@ process FASTP {
             2> ${prefix}.fastp.log \\
         | gzip -c > ${prefix}.fastp.fastq.gz
 
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
+        END_VERSIONS
+        """
+    } else if (meta.single_end) {
+        """
+        [ ! -f  ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz
+
+        fastp \\
+            --stdout \\
+            --in1 ${prefix}.fastq.gz \\
+            --out1  ${prefix}.fastp.fastq.gz \\
+            --thread $task.cpus \\
+            --json ${prefix}.fastp.json \\
+            --html ${prefix}.fastp.html \\
+            $fail_fastq \\
+            $args \\
+            2> ${prefix}.fastp.log
+
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
             fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
         END_VERSIONS
         """
     } else {
-        def fail_fastq  = save_trimmed_fail ? "--unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : ''
         def merge_fastq = save_merged ? "-m --merged_out ${prefix}.merged.fastq.gz" : ''
         """
         [ ! -f  ${prefix}_1.fastq.gz ] && ln -sf ${reads[0]} ${prefix}_1.fastq.gz
@@ -69,7 +88,6 @@ process FASTP {
             --detect_adapter_for_pe \\
             $args \\
             2> ${prefix}.fastp.log
-            
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":

modules/nf-core/modules/fastp/meta.yml

@@ -21,7 +21,8 @@ input:
       type: file
       description: |
         List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-        respectively.
+        respectively. If you wish to run interleaved paired-end data,  supply as single-end data
+        but with `--interleaved_in` in your `modules.conf`'s `ext.args` for the module.
   - save_trimmed_fail:
       type: boolean
       description: Specify true to save files that failed to pass trimming thresholds ending in `*.fail.fastq.gz`