Merge pull request #129 from JoseEspinosa/dev

Update modules, bump multiqc version and other minor fixes
nf-core · Feb 14, 2022 · e5989ae · e5989ae
2 parents 005aaf5 + 3cb9eb4
commit e5989ae
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Showing 18 changed files with 139 additions and 62 deletions.
diff --git a/.github/workflows/linting.yml b/.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
-
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -6,3 +6,4 @@ lint:
     - assets/email_template.txt
     - lib/NfcoreTemplate.groovy
     - assets/multiqc_config.yaml
+    - .github/workflows/linting.yml
diff --git a/.yamllint.yml b/.yamllint.yml
@@ -0,0 +1,5 @@
+extends: default
+
+rules:
+    document-start: disable
+    line-length: disable
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,25 +1,66 @@
 # nf-core/smrnaseq: Changelog
 
-## v2.0.0dev - [2021-09-15]
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unpublished Version / DEV]
+
+### Major enhancements
 
 * Port pipeline to the updated Nextflow DSL2 syntax adopted on nf-core/modules
     * Removed `--publish_dir_mode` as it is no longer required for the new syntax
-* Bump minimum Nextflow version from `21.04.0` -> `21.10.3`
+* Bump minimum Nextflow version from `20.04.0` -> `21.10.3`
 * Updated pipeline template to [nf-core/tools 2.2](https://github.com/nf-core/tools/releases/tag/2.2)
 * Point to the proper test data branch
 * Update mirtop container
 * Software version(s) will now be reported for every module imported during a given pipeline execution
-* Adapted DSL 2.0
 * Updated `nextflow_schema.json` should now display correctly on Nextflow Tower
 * Added mirtop logs to multiqc
-
-## [v1.2.0dev](https://github.com/nf-core/smrnaseq/releases/tag/1.2.0)
-
-### Added
-
 * Allow a gene to be associated to a non null number of reads in all samples (in `edgeR_miRBase.r` script)
 
-### Packaged software updates
+### Other enhancements & fixes
+
+### Parameters
+
+| Old parameter                | New parameter              |
+|------------------------------|----------------------------|
+| `--clusterOptions`           |                            |
+| `--conda`                    | `--enable_conda`           |
+
+> **NB:** Parameter has been **updated** if both old and new parameter information is present.
+> **NB:** Parameter has been **added** if just the new parameter information is present.
+> **NB:** Parameter has been **removed** if parameter information isn't present.
+
+### Software dependencies
+
+Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.
+
+| Dependency           | Old version  | New version |
+|----------------------|--------------|-------------|
+| `bioconductor-edger` | 3.26.5       | 3.36.0      |
+| `bioconductor-limma` | 3.40.2       |3.50.0      |
+| `mirdeep2`           | 2.0.1.2      | 2.0.1.3     |
+| `mirtop`             | 0.4.23       | 0.4.24      |
+| `multiqc`            | 1.10.1       | 1.12.0      |
+| `python`             | 3.7.3        | 3.8.3       |
+| `r-base`             | 3.6.3        | 4.0.3       |
+| `r-data.table`       | 1.12.4       | 1.14.2      |
+| `r-gplots`           | 3.0.1.1      | 3.1.1       |
+| `r-statmod`          | 1.4.32       | 1.4.36      |
+| `samtools`           | 1.12         | 1.13        |
+| `seqcluster`         | 1.2.7        | 1.2.8       |
+| `seqkit`             | 0.16.0       | 2.0.0       |
+| `trim-galore`        | 0.6.6        | 0.6.7       |
+| `bioconvert`         | -            | 0.4.3       |
+| `htseq`              | -            | -           |
+| `markdown`           | -            | -           |
+| `pymdown-extensions` | -            | -           |
+| `pygments`           | -            | -           |
+| `r-r.methodss3`      | -            | -           |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present.
+> **NB:** Dependency has been **added** if just the new version information is present.
+> **NB:** Dependency has been **removed** if version information isn't present.
 
 ## [v1.1.0](https://github.com/nf-core/smrnaseq/releases/tag/1.1.0) - 2021-06-15
 

diff --git a/conf/modules.config b/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" },

diff --git a/docs/output.md b/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.

diff --git a/docs/usage.md b/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 {

diff --git a/modules.json b/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"
             }
         }
     }

diff --git a/modules/nf-core/modules/cat/fastq/main.nf b/modules/nf-core/modules/cat/fastq/main.nf
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf b/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf
diff --git a/modules/nf-core/modules/fastqc/main.nf b/modules/nf-core/modules/fastqc/main.nf
diff --git a/modules/nf-core/modules/multiqc/main.nf b/modules/nf-core/modules/multiqc/main.nf