Update modules, bump multiqc version and other minor fixes

.github/workflows/linting.yml

@@ -12,9 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - uses: actions/setup-node@v1
-        with:
-          node-version: '10'
+      - uses: actions/setup-node@v2
       - name: Install markdownlint
         run: npm install -g markdownlint-cli
       - name: Run Markdownlint
@@ -27,21 +25,16 @@ jobs:
         with:
           message: |
             ## Markdown linting is failing
-
             To keep the code consistent with lots of contributors, we run automated code consistency checks.
             To fix this CI test, please run:
-
             * Install `markdownlint-cli`
                 * On Mac: `brew install markdownlint-cli`
                 * Everything else: [Install `npm`](https://www.npmjs.com/get-npm) then [install `markdownlint-cli`](https://www.npmjs.com/package/markdownlint-cli) (`npm install -g markdownlint-cli`)
             * Fix the markdown errors
                 * Automatically: `markdownlint . --fix`
                 * Manually resolve anything left from `markdownlint .`
-
             Once you push these changes the test should pass, and you can hide this comment :+1:
-
             We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
-
             Thanks again for your contribution!
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           allow-repeats: false
@@ -51,9 +44,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: actions/setup-node@v1
-        with:
-          node-version: '10'
+      - uses: actions/setup-node@v2
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -65,13 +56,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v1
-      - uses: actions/setup-node@v1
-        with:
-          node-version: '10'
+      - uses: actions/setup-node@v2
       - name: Install yaml-lint
         run: npm install -g yaml-lint
       - name: Run yaml-lint
-        run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml" -o -name "*.yaml")
+        run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml" -o -name "*.yaml") -c ${GITHUB_WORKSPACE}/.markdownlint.yml
 
       # If the above check failed, post a comment on the PR explaining the failure
       - name: Post PR comment
@@ -80,20 +69,15 @@ jobs:
         with:
           message: |
             ## YAML linting is failing
-
             To keep the code consistent with lots of contributors, we run automated code consistency checks.
             To fix this CI test, please run:
-
             * Install `yaml-lint`
                 * [Install `npm`](https://www.npmjs.com/get-npm) then [install `yaml-lint`](https://www.npmjs.com/package/yaml-lint) (`npm install -g yaml-lint`)
             * Fix the markdown errors
                 * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml")`
                 * Fix any reported errors in your YAML files
-
             Once you push these changes the test should pass, and you can hide this comment :+1:
-
             We highly recommend setting up yaml-lint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
-
             Thanks again for your contribution!
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           allow-repeats: false
@@ -111,7 +95,6 @@ jobs:
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
-
       - uses: actions/setup-python@v1
         with:
           python-version: '3.6'
@@ -121,7 +104,6 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install nf-core
-
       - name: Run nf-core lint
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
@@ -142,4 +124,3 @@ jobs:
             lint_log.txt
             lint_results.md
             PR_number.txt
-

.nf-core.yml

@@ -6,3 +6,4 @@ lint:
     - assets/email_template.txt
     - lib/NfcoreTemplate.groovy
     - assets/multiqc_config.yaml
+    - .github/workflows/linting.yml

.yamllint.yml

@@ -0,0 +1,5 @@
+extends: default
+
+rules:
+    document-start: disable
+    line-length: disable

conf/modules.config

@@ -29,7 +29,7 @@ process {
         ]
     }
 
-    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
+    withName: 'CUSTOM_DUMPSOFTWAREVERSIONS' {
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },
             mode: 'copy',
@@ -43,15 +43,15 @@ process {
 //
 
 process {
-    withName: CAT_FASTQ {
+    withName: 'CAT_FASTQ' {
         publishDir = [
             path: { "${params.outdir}/fastq" },
             mode: 'copy',
             pattern: '*.fastq',
             // enabled: params.save_merged_fastq //TODO ? implement save_merged_fastq param
         ]
     }
-    withName: INDEX_GENOME {
+    withName: 'INDEX_GENOME' {
         publishDir = [
             path: { "${params.outdir}/index" },
             mode: 'copy',
@@ -65,7 +65,7 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-    withName: EDGER_QC {
+    withName: 'EDGER_QC' {
         publishDir = [
             path: { "${params.outdir}/edger" },
             enabled: true
@@ -77,7 +77,7 @@ process {
 // Read QC and trimming options
 //
 process {
-    withName: MIRTRACE_RUN {
+    withName: 'MIRTRACE_RUN' {
         publishDir = [
             path: { "${params.outdir}/mirtrace" },
             mode: 'copy',
@@ -155,13 +155,13 @@ process {
             pattern: "unmapped/*.gz"
         ]
     }
-    withName: SEQCLUSTER_SEQUENCES {
+    withName: 'SEQCLUSTER_SEQUENCES' {
         publishDir = [
             path: { "${params.outdir}/seqcluster" },
             enabled: false
         ]
     }
-    withName: MIRTOP_QUANT {
+    withName: 'MIRTOP_QUANT' {
         publishDir = [
             path: { "${params.outdir}" },
             mode: 'copy',
@@ -175,10 +175,10 @@ process {
             pattern: "*.tsv"
         ]
     }
-    withName: EDGER_QC {
+    withName: 'EDGER_QC' {
         publishDir = [
             path: { "${params.outdir}/edger" },
-            enabled: false
+            enabled: true
         ]
     }
 }
@@ -216,7 +216,7 @@ if (fasta) {
 
     if (!params.skip_mirdeep) {
         process {
-            withName: MIRDEEP2_MAPPER {
+            withName: 'MIRDEEP2_MAPPER' {
                 publishDir = [
                     path: { "${params.outdir}/mirdeep" },
                     mode: 'copy',
@@ -229,7 +229,7 @@ if (fasta) {
 
 if (!params.skip_multiqc) {
     process {
-        withName: MULTIQC {
+        withName: 'MULTIQC' {
             ext.args   = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
             publishDir = [
                 path: { "${params.outdir}/multiqc" },

docs/output.md

@@ -65,7 +65,7 @@ This is an example of the output we can get:
 **Output directory: `results/samtools`**
 
 * `sample_mature.bam`: The aligned BAM file of alignment against mature miRNAs
-* `sample_mature_unmapped.fq.gz`: Unmapped reads against mature miRNAs *This file will be used as input for the alignment against miRNA precursors (hairpins)*
+* `sample_mature_unmapped.fq.gz`: Unmapped reads against mature miRNAs _This file will be used as input for the alignment against miRNA precursors (hairpins)_
 * `sample_mature_hairpin.bam`: The aligned BAM file of alignment against miRNA precursors (hairpins) that didn't map to the mature
 * `sample_mature_hairpin_unmapped.fq.gz`: Unmapped reads against miRNA precursors (hairpins)
 * `sample_mature_hairpin_genome.bam`: The aligned BAM file of alignment against that didn't map to the precursor.

docs/usage.md

@@ -197,7 +197,7 @@ Work dir:
 Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
 ```
 
-To bypass this error you would need to find exactly which resources are set by the `STAR_ALIGN` process. The quickest way is to search for `process STAR_ALIGN` in the [nf-core/rnaseq Github repo](https://github.com/nf-core/rnaseq/search?q=process+STAR_ALIGN). We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so based on the search results the file we want is `modules/nf-core/software/star/align/main.nf`. If you click on the link to that file you will notice that there is a `label` directive at the top of the module that is set to [`label process_high`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L9). The [Nextflow `label`](https://www.nextflow.io/docs/latest/process.html#label) directive allows us to organise workflow processes in separate groups which can be referenced in a configuration file to select and configure subset of processes having similar computing requirements. The default values for the `process_high` label are set in the pipeline's [`base.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L33-L37) which in this case is defined as 72GB. Providing you haven't set any other standard nf-core parameters to __cap__ the [maximum resources](https://nf-co.re/usage/configuration#max-resources) used by the pipeline then we can try and bypass the `STAR_ALIGN` process failure by creating a custom config file that sets at least 72GB of memory, in this case increased to 100GB. The custom config below can then be provided to the pipeline via the [`-c`](#-c) parameter as highlighted in previous sections.
+To bypass this error you would need to find exactly which resources are set by the `STAR_ALIGN` process. The quickest way is to search for `process STAR_ALIGN` in the [nf-core/rnaseq Github repo](https://github.com/nf-core/rnaseq/search?q=process+STAR_ALIGN). We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so based on the search results the file we want is `modules/nf-core/software/star/align/main.nf`. If you click on the link to that file you will notice that there is a `label` directive at the top of the module that is set to [`label process_high`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L9). The [Nextflow `label`](https://www.nextflow.io/docs/latest/process.html#label) directive allows us to organise workflow processes in separate groups which can be referenced in a configuration file to select and configure subset of processes having similar computing requirements. The default values for the `process_high` label are set in the pipeline's [`base.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L33-L37) which in this case is defined as 72GB. Providing you haven't set any other standard nf-core parameters to **cap** the [maximum resources](https://nf-co.re/usage/configuration#max-resources) used by the pipeline then we can try and bypass the `STAR_ALIGN` process failure by creating a custom config file that sets at least 72GB of memory, in this case increased to 100GB. The custom config below can then be provided to the pipeline via the [`-c`](#-c) parameter as highlighted in previous sections.
 
 ```nextflow
 process {

modules.json

@@ -4,34 +4,34 @@
     "repos": {
         "nf-core/modules": {
             "cat/fastq": {
-                "git_sha": "826a5603db5cf5b4f1e55cef9cc0b7c37d3c7e70"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "custom/dumpsoftwareversions": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "fastqc": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "multiqc": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "d1f33be04f5d3e402398707037f56f13166df4fe"
             },
             "samtools/flagstat": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "samtools/idxstats": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "samtools/index": {
-                "git_sha": "0fafaeebf52cc5ab554b83297ed02a48d852a848"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "samtools/sort": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "samtools/stats": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "trimgalore": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             }
         }
     }