Merge pull request #175 from LouisLeNezet/template_3.2.0

Update to 3.2.0 and add json support

Author: LouisLeNezet

.github/workflows/linting_comment.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@80620a5d27ce0ae443b965134db88467fc607b43 # v7
+        uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8
         with:
           workflow: linting.yml
           workflow_conclusion: completed

.github/workflows/release-announcements.yml

@@ -27,39 +27,6 @@ jobs:
 
             ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
 
-  send-tweet:
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
-        with:
-          python-version: "3.10"
-      - name: Install dependencies
-        run: pip install tweepy==4.14.0
-      - name: Send tweet
-        shell: python
-        run: |
-          import os
-          import tweepy
-
-          client = tweepy.Client(
-              access_token=os.getenv("TWITTER_ACCESS_TOKEN"),
-              access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"),
-              consumer_key=os.getenv("TWITTER_CONSUMER_KEY"),
-              consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"),
-          )
-          tweet = os.getenv("TWEET")
-          client.create_tweet(text=tweet)
-        env:
-          TWEET: |
-            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
-
-            Please see the changelog: ${{ github.event.release.html_url }}
-          TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }}
-          TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }}
-          TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }}
-          TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}
-
   bsky-post:
     runs-on: ubuntu-latest
     steps:

.nf-core.yml

@@ -1,4 +1,4 @@
-nf_core_version: 3.1.2
+nf_core_version: 3.2.0
 repository_type: pipeline
 template:
   author: Louis Le Nezet, Anabella Trigila

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ repos:
           - [email protected]
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "3.0.3"
+    rev: "3.1.2"
     hooks:
       - id: editorconfig-checker
         alias: ec

CHANGELOG.md

@@ -7,10 +7,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#175](https://github.com/nf-core/phaseimpute/pull/175) - Add support for all input files in `.json` or `.yaml` format.
+
 ### `Changed`
 
 - [#166](https://github.com/nf-core/phaseimpute/pull/166) - Bump version to 1.1.0dev and update `CHANGELOG.md`.
 - [#170](https://github.com/nf-core/phaseimpute/pull/170) - Update TEMPLATE to nf-core tools version 3.1.2.
+- [#175](https://github.com/nf-core/phaseimpute/pull/175) - Update TEMPLATE to nf-core tools version 3.2.0. Move `CHRCHECK` functions to the workflow directory.
 
 ### `Fixed`
 
@@ -79,7 +82,7 @@ Special thanks to [Matthias Hörtenhuber](https://github.com/mashehu), [Mazzalab
 - [#157](https://github.com/nf-core/phaseimpute/pull/157) - Add `chunk_model` as parameter for better control over `GLIMPSE2_CHUNK` and set window size in `GLIMPSE1_CHUNK` and `GLIMPSE2_chunk` to 4mb to reduce number of chunks (empirical).
 - [#160](https://github.com/nf-core/phaseimpute/pull/160) - Improve `CHANGELOG.md` and add details to `usage.md`
 - [#158](https://github.com/nf-core/phaseimpute/pull/158) - Remove frequency computation and phasing from full test to reduce cost and computational time.
-- [#164](https://github.com/nf-core/phaseimpute/pull/164) - Rename `BAM_REGION_SAMTOOLS` to `BAM_EXTRACT_REGION_SAMTOOLS`. Remove `GLIMPSE2_SPLITREFERENCE` as it is not used. Add more steps to `test_all` profile for more exhaustivity.
+- [#164](https://github.com/nf-core/phaseimpute/pull/164) - Rename `BAM_REGION_SAMTOOLS` to `BAM_EXTRACT_REGION_SAMTOOLS`. Remove `GLIMPSE2_SPLITREFERENCE` as it is not used. Add more steps to `test_all` profile for more exhaustiveness.
 - [#163](https://github.com/nf-core/phaseimpute/pull/163) - Improve configuration for demanding processes. Use Genome in a Bottle VCF benchmarking file for AWS full test. Moved from `glimpse1` to `glimpse2` for the full test profile.
 - [#165](https://github.com/nf-core/phaseimpute/pull/165) - Update metro map and add logo to the documentation.
 
@@ -96,7 +99,7 @@ Special thanks to [Matthias Hörtenhuber](https://github.com/mashehu), [Mazzalab
 - [#161](https://github.com/nf-core/phaseimpute/pull/161) - Fix `VCF_SPLIT_BCFTOOLS` when only one sample present by updating `BCFTOOLS_PLUGINSPLIT` and adding `BCFTOOLS_QUERY` to get truth samples names for renaming the resulting files.
 - [#162](https://github.com/nf-core/phaseimpute/pull/162) - Fix `fai` usage when provided by `genomes` parameter.
 - [#164](https://github.com/nf-core/phaseimpute/pull/164) - Improve documentation writing
-- [#163](https://github.com/nf-core/phaseimpute/pull/163) - Fix MULTIQC samples names (add post-processing for clean up `FILTER_CHR_DWN`, `FILTER_CHR_INP`, `GAWK_ERROR_SPL`, `GAWK_RSQUARE_SPL`). Fix output panel `publisDir`. Fix java version to `17` in `ci.yml` due to new nextflow version.
+- [#163](https://github.com/nf-core/phaseimpute/pull/163) - Fix MULTIQC samples names (add post-processing for clean up `FILTER_CHR_DWN`, `FILTER_CHR_INP`, `GAWK_ERROR_SPL`, `GAWK_RSQUARE_SPL`). Fix output panel `publishDir`. Fix java version to `17` in `ci.yml` due to new nextflow version.
 
 ### `Dependencies`
 

modules.json

@@ -119,7 +119,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
+                        "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",
                         "installed_by": ["modules"]
                     },
                     "quilt/quilt": {

modules/nf-core/multiqc/environment.yml

@@ -276,14 +276,14 @@ env {
 }
 
 // Set bash options
-process.shell = """\
-bash
-
-set -e # Exit if a tool returns a non-zero status/exit code
-set -u # Treat unset variables and parameters as an error
-set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
-set -C # No clobber - prevent output redirection from overwriting files.
-"""
+process.shell = [
+    "bash",
+    "-C",         // No clobber - prevent output redirection from overwriting files.
+    "-e",         // Exit if a tool returns a non-zero status/exit code
+    "-u",         // Treat unset variables and parameters as an error
+    "-o",         // Returns the status of the last command to exit..
+    "pipefail"    //   ..with a non-zero status or zero if all successfully execute
+]
 
 // Disable process selector warnings by default. Use debug profile to enable warnings.
 nextflow.enable.configProcessNamesValidation = false

modules/nf-core/multiqc/main.nf

@@ -18,7 +18,7 @@
                     "exists": true,
                     "schema": "assets/schema_input.json",
                     "mimetype": "text/csv",
-                    "pattern": "^\\S+\\.csv$",
+                    "pattern": "^\\S+\\.(csv|tsv|yaml|json)$",
                     "description": "Path to comma-separated file containing information about the samples in the experiment.",
                     "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/phaseimpute/usage#samplesheet-input).",
                     "fa_icon": "fas fa-file-csv"
@@ -28,7 +28,7 @@
                     "description": "Region of the genome to use (optional: if no file given, the whole genome will be used). The file should be a comma-separated file with 3 columns, and a header row.",
                     "schema": "assets/schema_input_region.json",
                     "format": "file-path",
-                    "pattern": "^\\S+\\.csv$"
+                    "pattern": "^\\S+\\.(csv|tsv|yaml|json)$"
                 },
                 "outdir": {
                     "type": "string",
@@ -94,7 +94,7 @@
                 "genotype": {
                     "type": "string",
                     "description": "Genotype position to use to simulate the data",
-                    "pattern": "^\\S+\\.(csv|tsv|txt)$",
+                    "pattern": "^\\S+\\.(csv|tsv|yaml|json)$",
                     "format": "file-path",
                     "mimetype": "text/csv"
                 }
@@ -112,7 +112,7 @@
                     "fa_icon": "far fa-file-code",
                     "format": "file-path",
                     "schema": "assets/schema_input_panel.json",
-                    "pattern": "^\\S+\\.(csv|tsv|txt)$",
+                    "pattern": "^\\S+\\.(csv|tsv|yaml|json)$",
                     "mimetype": "text/csv"
                 },
                 "phase": {
@@ -155,7 +155,15 @@
                     "format": "file-path",
                     "mimetype": "text/csv",
                     "schema": "/assets/schema_chunks.json",
-                    "pattern": "^\\S+\\.csv$"
+                    "pattern": "^\\S+\\.(csv|tsv|yaml|json)$"
+                },
+                "posfile": {
+                    "type": "string",
+                    "description": "Path to comma-separated file containing tab-separated files describing the variable positions to be used for imputation. Refer to the documentation for the `--posfile` argument of STITCH for more information.",
+                    "format": "file-path",
+                    "schema": "assets/schema_posfile.json",
+                    "pattern": "^\\S+\\.(csv|tsv|yaml|json)$",
+                    "mimetype": "text/csv"
                 },
                 "seed": {
                     "type": "integer",
@@ -177,7 +185,7 @@
                     "exists": true,
                     "schema": "assets/schema_input.json",
                     "mimetype": "text/csv",
-                    "pattern": "^\\S+\\.csv$",
+                    "pattern": "^\\S+\\.(csv|tsv|yaml|json)$",
                     "description": "Path to comma-separated file containing information about the samples truth files in the experiment.",
                     "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/phaseimpute/usage#samplesheet-input).",
                     "fa_icon": "fas fa-file-csv"
@@ -441,14 +449,6 @@
             "description": "Arguments to customize STITCH run",
             "default": "",
             "properties": {
-                "posfile": {
-                    "type": "string",
-                    "description": "Path to comma-separated file containing tab-separated files describing the variable positions to be used for imputation. Refer to the documentation for the `--posfile` argument of STITCH for more information.",
-                    "format": "file-path",
-                    "schema": "assets/schema_posfile.json",
-                    "pattern": "^\\S+\\.(csv|tsv|txt)$",
-                    "mimetype": "text/csv"
-                },
                 "k_val": {
                     "type": "integer",
                     "default": 2,