Important! Template update for nf-core/tools v2.11.1

.devcontainer/devcontainer.json

@@ -18,11 +18,11 @@
                 "python.linting.flake8Path": "/opt/conda/bin/flake8",
                 "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
                 "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
-                "python.linting.pylintPath": "/opt/conda/bin/pylint"
+                "python.linting.pylintPath": "/opt/conda/bin/pylint",
             },
 
             // Add the IDs of extensions you want installed when the container is created.
-            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
-        }
-    }
+            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"],
+        },
+    },
 }

.github/CONTRIBUTING.md

@@ -27,6 +27,9 @@ If you're not used to this workflow with git, you can start with some [docs from
 
 ## Tests
 
+You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to
+receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir <OUTDIR>`.
+
 When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
 Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -19,6 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/cris
 - [ ] If necessary, also make a PR on the nf-core/crisprseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
+- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `CHANGELOG.md` is updated.

.github/workflows/ci.yml

@@ -35,7 +35,7 @@ jobs:
 
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1

.github/workflows/fix-linting.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -24,7 +24,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php

.github/workflows/linting.yml

@@ -14,9 +14,9 @@ jobs:
   EditorConfig:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -27,9 +27,9 @@ jobs:
   Prettier:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install Prettier
         run: npm install -g prettier
@@ -40,7 +40,7 @@ jobs:
   PythonBlack:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Check code lints with Black
         uses: psf/black@stable
@@ -71,7 +71,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1

.gitpod.yml

@@ -4,7 +4,9 @@ tasks:
     command: |
       pre-commit install --install-hooks
       nextflow self-update
-
+  - name: unset JAVA_TOOL_OPTIONS
+    command: |
+      unset JAVA_TOOL_OPTIONS
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
     - codezombiech.gitignore # Language support for .gitignore files

CHANGELOG.md

@@ -5,20 +5,23 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [v2.2.0dev]
 
+### Added
+
+- Template update to 2.11.1 ([#105](https://github.com/nf-core/crisprseq/pull/105))
+
 ## [v2.1.1 - Jamon Salas - patch](https://github.com/nf-core/crisprseq/releases/tag/2.1.1) - [14.12.2023]
 
 ### Added
 
 - Update all modules to the last version in nf-core/modules ([#92](https://github.com/nf-core/crisprseq/pull/92))
-- More documentation for screening analysis.  ([#99](https://github.com/nf-core/crisprseq/pull/99))
+- More documentation for screening analysis. ([#99](https://github.com/nf-core/crisprseq/pull/99))
 - Contrasts are now given under a different flag and MAGeCK MLE and BAGEL2 are automatically run instead of MAGeCK RRA. ([#99](https://github.com/nf-core/crisprseq/pull/99))
 - Added cutadapt for screening analysis ([#95](https://github.com/nf-core/crisprseq/pull/95))
 
 ### Fixed
 
 - Fixed paired-end for screening analysis ([#94](https://github.com/nf-core/crisprseq/pull/94))
 
-
 ## [v2.1.0 - Jamon Salas](https://github.com/nf-core/crisprseq/releases/tag/2.1.0) - [14.11.2023]
 
 ### Added

README.md

@@ -66,11 +66,8 @@ For crispr screening:
 
 ## Usage
 
-:::note
-If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how
-to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)
-with `-profile test` before running the workflow on actual data.
-:::
+> [!NOTE]
+> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
 
 First, prepare a samplesheet with your input data that looks as follows:
 
@@ -98,11 +95,9 @@ Now, you can run the pipeline using:
 nextflow run nf-core/crisprseq --input samplesheet.csv --analysis <targeted/screening> --outdir <OUTDIR> -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
 ```
 
-:::warning
-Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
-provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
-see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
-:::
+> [!WARNING]
+> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
+> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
 
 For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/crisprseq/usage) and the [parameter documentation](https://nf-co.re/crisprseq/parameters).
 

assets/multiqc_config.yml

@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/crisprseq/releases/tag/dev" target="_blank">nf-core/crisprseq</a>
+  This report has been generated by the <a href="https://github.com/nf-core/crisprseq/tree/dev" target="_blank">nf-core/crisprseq</a>
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://nf-co.re/crisprseq/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:

assets/slackreport.json

@@ -3,7 +3,7 @@
         {
             "fallback": "Plain-text summary of the attachment.",
             "color": "<% if (success) { %>good<% } else { %>danger<%} %>",
-            "author_name": "nf-core/crisprseq v${version} - ${runName}",
+            "author_name": "nf-core/crisprseq ${version} - ${runName}",
             "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
             "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
             "fields": [

conf/modules.config

@@ -122,6 +122,10 @@ process {
         ]
     }
 
+    withName: MAGECK_GRAPHRRA {
+        containerOptions = ''
+    }
+
     withName: CRISPRCLEANR_NORMALIZE {
         publishDir       = [
             path: { "${params.outdir}/crisprcleanr/normalization/" },
@@ -308,7 +312,7 @@ process {
     }
 
     withName: 'MULTIQC' {
-        ext.args   = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
+        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
             path: { "${params.outdir}/multiqc" },
             mode: params.publish_dir_mode,

conf/test_screening.config

@@ -26,3 +26,9 @@ params {
     library           = "https://raw.githubusercontent.com/nf-core/test-datasets/crisprseq/testdata/brunello_target_sequence.txt"
     contrasts         = "https://raw.githubusercontent.com/nf-core/test-datasets/crisprseq/testdata/rra_contrasts.txt"
 }
+
+process {
+    withName: BAGEL2_BF {
+        ext.args = '-s 3' // Seed to avoid random errors due to a too small sample
+    }
+}

conf/test_screening_full.config

@@ -21,3 +21,9 @@ params {
     mle_design_matrix = "https://raw.githubusercontent.com/nf-core/test-datasets/crisprseq/testdata/full_test/drugA_drugB_vs_treatment.txt"
     library           = "https://raw.githubusercontent.com/nf-core/test-datasets/crisprseq/testdata/brunello_target_sequence.txt"
 }
+
+process {
+    withName: BAGEL2_BF {
+        ext.args = '-s 3' // Seed to avoid random errors due to a too small sample
+    }
+}

conf/test_screening_paired.config

@@ -24,3 +24,9 @@ params {
     analysis          = 'screening'
     library           = "https://raw.githubusercontent.com/nf-core/test-datasets/crisprseq/testdata/brunello_target_sequence.txt"
 }
+
+process {
+    withName: BAGEL2_BF {
+        ext.args = '-s 3' // Seed to avoid random errors due to a too small sample
+    }
+}

conf/test_screening_rra.config

@@ -27,3 +27,9 @@ params {
     contrasts         = "https://raw.githubusercontent.com/nf-core/test-datasets/crisprseq/testdata/rra_contrasts.txt"
     rra               = true
 }
+
+process {
+    withName: BAGEL2_BF {
+        ext.args = '-s 3' // Seed to avoid random errors due to a too small sample
+    }
+}

docs/usage/screening.md

@@ -21,7 +21,7 @@ nextflow run nf-core/crisprseq --analysis screening --input samplesheet.csv --li
 ```
 
 The following required parameters are here described.
- If you wish to input a raw count or normalized table, you can skip the samplesheet parameter as well as the library one and directly input your table using count_table `--count_table your_count_table`. If your count table is normalized, be sure to set the normalization method to none in MAGeCK MLE or MAGeCK RRA using a config file.
+If you wish to input a raw count or normalized table, you can skip the samplesheet parameter as well as the library one and directly input your table using count_table `--count_table your_count_table`. If your count table is normalized, be sure to set the normalization method to none in MAGeCK MLE or MAGeCK RRA using a config file.
 
 ### Full samplesheet
 
@@ -42,7 +42,6 @@ SRR8983580,SRR8983580.small.fastq.gz,,treatment
 
 An [example samplesheet](https://github.com/nf-core/test-datasets/blob/crisprseq/testdata/samplesheet_test.csv) has been provided with the pipeline.
 
-
 ### cutadapt
 
 MAGeCK count which is the main alignment software used is normally able to automatically determine the trimming length and sgRNA length, in most cases. Therefore, you don't need to go to this step unless MAGeCK fails to do so by itself. If the nucleotide length in front of sgRNA varies between different reads, you can use cutadapt to remove the adaptor sequences by using the flag `--cutadapt ADAPTER`.
@@ -61,7 +60,6 @@ We recommend to run MAGeCK MLE and BAGEL2 as these are the most used and most re
 
 CRISPRcleanR is used for gene count normalization and the removal of biases for genomic segments for which copy numbers are amplified. Currently, the pipeline only supports annotation libraries already present in the R package and which can be found [here](https://github.com/francescojm/CRISPRcleanR/blob/master/Reference_Manual.pdf). To use CRISPRcleanR normalization, use `--crisprcleanr library`, `library` being the exact name as the library in the CRISPRcleanR documentation (e.g: "AVANA_Library").
 
-
 ### Running MAGeCK MLE and BAGEL2 with a contrast file
 
 To run both MAGeCK MLE and BAGEL2, you can provide a contrast file with the flag `--contrasts` with the mandatory headers "treatment" and "reference". These two columns should be separated with a dot comma (;) and contain the `csv` extension. You can also integrate several samples/conditions by comma separating them in each column. Please find an example here below :
@@ -75,7 +73,7 @@ A full example can be found [here](https://raw.githubusercontent.com/nf-core/tes
 
 ### Running MAGeCK RRA only
 
-MAGeCK RRA performs robust ranking aggregation to identify genes that are consistently ranked highly across multiple replicate screens. To run MAGeCK rra, you can define the contrasts as previously stated in the last section and also specify  `--rra` .
+MAGeCK RRA performs robust ranking aggregation to identify genes that are consistently ranked highly across multiple replicate screens. To run MAGeCK rra, you can define the contrasts as previously stated in the last section and also specify `--rra` .
 
 ### Running MAGeCK MLE only
 

modules.json

@@ -49,7 +49,7 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53",
                         "installed_by": ["modules"]
                     },
                     "mageck/count": {
@@ -89,7 +89,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "214d575774c172062924ad3564b4f66655600730",
+                        "git_sha": "4ab13872435962dadc239979554d13709e20bf29",
                         "installed_by": ["modules"]
                     },
                     "pear": {

modules/local/bagel2/graph.nf

@@ -64,8 +64,8 @@ process BAGEL2_GRAPH {
     # alas, no `pyyaml` pre-installed in the cellranger container
     with open("versions.yml", "w") as f:
         f.write('"${task.process}":\\n')
-        f.write(f'  pandas: "{version}"\\n')
-        f.write(f'  matplotlib.pyplot: "{matplotlib_version}"\\n')
+        f.write(f'  pandas: {version}\\n')
+        f.write(f'  matplotlib.pyplot: {matplotlib_version}\\n')
 
     """
 

modules/local/bagel2/pr.nf

@@ -26,9 +26,9 @@ process BAGEL2_PR {
     BAGEL.py pr -i $bf  -o '${meta.treatment}_vs_${meta.reference}.pr' -e $reference_essentials -n $reference_nonessentials $args
 
     cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            python: \$(python --version | sed 's/Python //g')
-            BAGEL2: \$( BAGEL.py version | grep -o 'Version: [0-9.]*' | awk '{print  \$2}' | grep -v '^\$')
+    "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
+        BAGEL2: \$( BAGEL.py version | grep -o 'Version: [0-9.]*' | awk '{print  \$2}' | grep -v '^\$')
     END_VERSIONS
     """