Merge branch 'nf-core-template-merge-3.1.2' into nf-core-template-merge-3.2.0

Author: Aratz

.github/CONTRIBUTING.md

@@ -82,6 +82,12 @@ If you wish to contribute a new step, please use the following coding standards:
 9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
 10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
 
+### Things to consider regarding displaying results for a new tool
+
+- If a MultiQC module exist for the tool, use the standard settings for it to start with.
+- If no Multiqc module exists, the results of the tool should be made available in the results directory.
+- If a tool doesn’t produce output files, the stdout should be channeled into a output file that can be accessible from the outdir of the pipeline.
+
 ### Default values
 
 Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`.

.github/workflows/nf-test.yml

@@ -0,0 +1,24 @@
+name: nf-test
+
+on: [push, pull_request]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Nextflow latest-edge
+        uses: nf-core/setup-nextflow@v2
+        with:
+          version: "latest-edge"
+
+      - name: Install nf-test
+        run: |
+          wget -qO- https://get.nf-test.com | bash
+          sudo mv nf-test /usr/local/bin/
+
+      - name: Run Tests
+        run: nf-test test --ci tests

.gitignore

@@ -7,3 +7,5 @@ testing/
 testing*
 *.pyc
 null/
+.nf-test
+.nf-test.log

CHANGELOG.md

@@ -9,8 +9,20 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 
 ### `Added`
 
+- [#68](https://github.com/nf-core/seqinspector/pull/68) Add tool selector
+- [#20](https://github.com/nf-core/seqinspector/pull/20) Use tags to generate group reports
+- [#13](https://github.com/nf-core/seqinspector/pull/13) Generate reports per run, per project and per lane.
+- [#49](https://github.com/nf-core/seqinspector/pull/49) Merge with template 3.0.2.
+- [#56](https://github.com/nf-core/seqinspector/pull/56) Added SeqFu stats module.
+- [#50](https://github.com/nf-core/seqinspector/pull/50) Add an optional subsampling step.
+- [#51](https://github.com/nf-core/seqinspector/pull/51) Add nf-test to CI.
+- [#63](https://github.com/nf-core/seqinspector/pull/63) Contribution guidelines added about displaying results for new tools
+- [#53](https://github.com/nf-core/seqinspector/pull/53) Add FastQ-Screen database multiplexing and limit scope of nf-test in CI.
+
 ### `Fixed`
 
+- [#71](https://github.com/nf-core/seqinspector/pull/71) FASTQSCREEN does not fail when multiple reads are provided.
+
 ### `Dependencies`
 
 ### `Deprecated`

CITATIONS.md

@@ -14,10 +14,20 @@
 
 > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
+- [SeqFu](https://telatin.github.io/seqfu2/)
+
+> Telatin A, Fariselli P, Birolo G. SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files. Bioengineering 2021, 8, 59. doi.org/10.3390/bioengineering8050059
+
+- [FastQ Screen](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)
+
+> Wingett SW and Andrews S. FastQ Screen: A tool for multi-genome mapping and quality control [version 2; referees: 4 approved]. F1000Research 2018, 7:1338 (https://doi.org/10.12688/f1000research.15931.2)
+
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
 > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
+- [Seqtk](https://github.com/lh3/seqtk)
+
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)

README.md

@@ -29,33 +29,30 @@
 
 <!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
      workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
-<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
+
+1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))
+2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
+3. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
 
 ## 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.
 
-<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
-     Explain what rows and columns represent. For instance (please edit as appropriate):
-
 First, prepare a samplesheet with your input data that looks as follows:
 
 `samplesheet.csv`:
 
 ```csv
-sample,fastq_1,fastq_2
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
+sample,fastq_1,fastq_2,rundir,tags
+CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2
 ```
 
 Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
 
--->
-
 Now, you can run the pipeline using:
 
-<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
-
 ```bash
 nextflow run nf-core/seqinspector \
    -profile <docker/singularity/.../institute> \
@@ -76,11 +73,11 @@ For more details about the output files and reports, please refer to the
 
 ## Credits
 
-nf-core/seqinspector was originally written by Adrien Coulier.
+nf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/).
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 
-<!-- TODO nf-core: If applicable, make list of people who have also contributed -->
+- [@mahesh-panchal](https://github.com/mahesh-panchal)
 
 ## Contributions and Support
 

assets/example_fastq_screen_references.csv

@@ -0,0 +1,4 @@
+name,dir,basename,aligner
+Ecoli,s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/Bowtie2Index/,genome,bowtie2
+PhiX,s3://ngi-igenomes/igenomes/PhiX/Illumina/RTA/Sequence/Bowtie2Index/,genome,bowtie2
+Scerevisiae,s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/NCBI/build3.1/Sequence/Bowtie2Index/,genome,bowtie2

assets/samplesheet.csv

@@ -1,3 +1,7 @@
-sample,fastq_1,fastq_2
-SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz
-SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,
+sample,fastq_1,fastq_2,rundir,tags
+SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz,/path/to/rundir,paired_sample:lane1
+SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A2_S2_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A2_S2_L002_R2_001.fastq.gz,/path/to/rundir,paired_sample:lane1
+SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A3_S3_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A3_S3_L002_R2_001.fastq.gz,/path/to/rundir,paired_sample:lane2
+SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,group1
+SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,group2
+SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,group3

assets/schema_fastq_screen_references.json

@@ -0,0 +1,35 @@
+{
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "$id": "https://raw.githubusercontent.com/nf-core/seqinspector/master/assets/schema_fastq_screen_references.json",
+    "title": "nf-core/seqinspector pipeline - params.fastq_screen_references schema",
+    "description": "Schema for the file provided with params.fastq_screen_references",
+    "type": "array",
+    "items": {
+        "type": "object",
+        "properties": {
+            "name": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "The reference name as referred to by FastQ Screen."
+            },
+            "dir": {
+                "type": "string",
+                "format": "file-path",
+                "exists": true,
+                "pattern": "^\\S+$",
+                "errorMessage": "Path to the dir containing the aligner reference and index. Can be remote."
+            },
+            "basename": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "The shared basename of the reference and index files contained in the dir."
+            },
+            "aligner": {
+                "type": "string",
+                "enum": ["bowtie", "bowtie2", "bwa", "minimap2"],
+                "errorMessage": "Specify the aligner to use for the mapping. Valid arguments are 'bowtie', bowtie2' (default), 'bwa' or 'minimap2'."
+            }
+        },
+        "required": ["name", "dir", "basename", "aligner"]
+    }
+}

assets/schema_input.json

@@ -11,7 +11,7 @@
                 "type": "string",
                 "pattern": "^\\S+$",
                 "errorMessage": "Sample name must be provided and cannot contain spaces",
-                "meta": ["id"]
+                "meta": ["sample"]
             },
             "fastq_1": {
                 "type": "string",
@@ -26,8 +26,24 @@
                 "exists": true,
                 "pattern": "^\\S+\\.f(ast)?q\\.gz$",
                 "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
+            },
+            "rundir": {
+                "type": "string",
+                "format": "path",
+                "exists": true,
+                "errorMessage": "Run directory must be a path",
+                "meta": ["rundir"]
+            },
+            "tags": {
+                "type": "string",
+                "pattern": "^([A-Za-z0-9_-]+:)*([A-Za-z0-9_-]+)$",
+                "errorMessage": "Tags must be separated by colons and only consist of lowercase letters, numbers, underscores and hyphens.",
+                "meta": ["tags"]
             }
         },
-        "required": ["sample", "fastq_1"]
+        "required": ["sample", "fastq_1"],
+        "dependentRequired": {
+            "fastq_2": ["fastq_1"]
+        }
     }
 }