nf-core · oligomyeggo · Nov 14, 2024
diff --git a/docs/output.md b/docs/output.md
@@ -18,6 +18,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
   - [Introduction](#introduction)
   - [Pipeline overview](#pipeline-overview)
   - [Preprocessing](#preprocessing)
+    - [fq lint](#fq-lint)
     - [cat](#cat)
     - [FastQC](#fastqc)
     - [UMI-tools extract](#umi-tools-extract)
@@ -61,6 +62,18 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 ## Preprocessing
 
+### fq lint
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `fq_lint/`
+  - `*.fq_lint.txt`: If `--save_linting_log` is specified, fq lint logs for each sample will be placed in this directory.
+
+</details>
+
+[fq lint](https://github.com/stjude-rust-labs/fq#lint) is a tool to validate both single-end and paired-end FastQ files.
+
 ### cat
 
 <details markdown="1">

diff --git a/docs/usage.md b/docs/usage.md
@@ -100,6 +100,10 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p
 
 > **NB:** The `group` and `replicate` columns were replaced with a single `sample` column as of v3.1 of the pipeline. The `sample` column is essentially a concatenation of the `group` and `replicate` columns, however it now also offers more flexibility in instances where replicate information is not required e.g. when sequencing clinical samples. If all values of `sample` have the same number of underscores, fields defined by these underscore-separated names may be used in the PCA plots produced by the pipeline, to regain the ability to represent different groupings.
 
+## FASTQ validation
+
+[fq lint](https://github.com/stjude-rust-labs/fq#lint) is a tool to validate FastQ files, and can be used to check input FastQ files before continuing with the rest of the pipeline. fq lint can be run on either single-end or paired-end FastQ files. By default, FastQ files are validated using all validators provided by fq lint, and the validator will panic on the first error it encounters. If an error is encountered, the pipeline will exit. Linting can be skipped by setting the `--skip_linting` parameter to `false`.
+
 ## FASTQ sampling
 
 If you would like to reduce the number of reads used in the analysis, for example to test pipeline operation with limited resource usage, you can make use of the FASTP option for trimming (see below). FASTP has an option to take the first `n` reads of input FASTQ file(s), so this can be used to reduce the reads passed to subsequent steps. For example, to pass only the first 10,000 reads for trimming you would set input paramters like:
@@ -153,9 +157,9 @@ The `--umitools_grouping_method` parameter affects [how similar, but non-identic
 | UMI type     | Source                                                                                                                                                                                                                                                                                                                              | Pipeline parameters                                                                                                                                                         |
 | ------------ | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | In read name | [Illumina BCL convert >3.7.5](https://emea.support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl_convert/bcl-convert-v3-7-5-software-guide-1000000163594-00.pdf)                                                                                                                     | `--with_umi --skip_umi_extract --umitools_umi_separator ":"`                                                                                                                |
-| In sequence  | [Lexogen QuantSeq® 3’ mRNA-Seq V2 FWD](https://www.lexogen.com/quantseq-3mrna-sequencing) + [UMI Second Strand Synthesis Module](https://faqs.lexogen.com/faq/how-can-i-add-umis-to-my-quantseq-libraries)                                                                                                                         | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern "^(?P<umi_1>.{6})(?P<discard_1>.{4}).*"`                                                                |
-| In sequence  | [Lexogen CORALL® Total RNA-Seq V1](https://www.lexogen.com/corall-total-rna-seq/)<br> > _mind [Appendix H](https://www.lexogen.com/wp-content/uploads/2020/04/095UG190V0130_CORALL-Total-RNA-Seq_2020-03-31.pdf) regarding optional trimming_                                                                                      | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern "^(?P<umi_1>.{12}).*"`<br>Optional: `--clip_r2 9 --three_prime_clip_r2 12`                              |
-| In sequence  | [Takara Bio SMARTer® Stranded Total RNA-Seq Kit v3](https://www.takarabio.com/documents/User%20Manual/SMARTer%20Stranded%20Total%20RNA/SMARTer%20Stranded%20Total%20RNA-Seq%20Kit%20v3%20-%20Pico%20Input%20Mammalian%20User%20Manual-a_114949.pdf)                                                                                | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern2 "^(?P<umi_1>.{8})(?P<discard_1>.{6}).*"`                                                               |
+| In sequence  | [Lexogen QuantSeq® 3’ mRNA-Seq V2 FWD](https://www.lexogen.com/quantseq-3mrna-sequencing) + [UMI Second Strand Synthesis Module](https://faqs.lexogen.com/faq/how-can-i-add-umis-to-my-quantseq-libraries)                                                                                                                          | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern "^(?P<umi_1>.{6})(?P<discard_1>.{4}).*"`                                                                |
+| In sequence  | [Lexogen CORALL® Total RNA-Seq V1](https://www.lexogen.com/corall-total-rna-seq/)<br> > _mind [Appendix H](https://www.lexogen.com/wp-content/uploads/2020/04/095UG190V0130_CORALL-Total-RNA-Seq_2020-03-31.pdf) regarding optional trimming_                                                                                       | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern "^(?P<umi_1>.{12}).*"`<br>Optional: `--clip_r2 9 --three_prime_clip_r2 12`                              |
+| In sequence  | [Takara Bio SMARTer® Stranded Total RNA-Seq Kit v3](https://www.takarabio.com/documents/User%20Manual/SMARTer%20Stranded%20Total%20RNA/SMARTer%20Stranded%20Total%20RNA-Seq%20Kit%20v3%20-%20Pico%20Input%20Mammalian%20User%20Manual-a_114949.pdf)                                                                                 | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern2 "^(?P<umi_1>.{8})(?P<discard_1>.{6}).*"`                                                               |
 | In sequence  | [Watchmaker mRNA Library Prep Kit](https://watchmakergenomics.com/wp-content/uploads/2023/11/M223_mRNA-Library-Prep-Kit-_UG_WMUG214_v1-1-0823.pdf) with [Twist UMI Adapter System](https://www.twistbioscience.com/sites/default/files/resources/2023-03/DOC-001337_TechNote-ProcessingSequencingDataUtilizingUMI-REV1-singles.pdf) | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern "^(?P<umi_1>.{5})(?P<discard_1>.{2}).*" --umitools_bc_pattern2 "^(?P<umi_2>.{5})(?P<discard_2>.{2}).*"` |
 
 > _No warranty for the accuracy or completeness of the parameters is implied_

diff --git a/modules.json b/modules.json
@@ -57,6 +57,11 @@
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"]
                     },
+                    "fq/lint": {
+                        "branch": "master",
+                        "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc",
+                        "installed_by": ["modules"]
+                    },
                     "fq/subsample": {
                         "branch": "master",
                         "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc",

diff --git a/modules/nf-core/fq/lint/environment.yml b/modules/nf-core/fq/lint/environment.yml
diff --git a/modules/nf-core/fq/lint/main.nf b/modules/nf-core/fq/lint/main.nf
diff --git a/modules/nf-core/fq/lint/meta.yml b/modules/nf-core/fq/lint/meta.yml
diff --git a/modules/nf-core/fq/lint/nextflow.config b/modules/nf-core/fq/lint/nextflow.config
diff --git a/modules/nf-core/fq/lint/tests/main.nf.test b/modules/nf-core/fq/lint/tests/main.nf.test
diff --git a/modules/nf-core/fq/lint/tests/main.nf.test.snap b/modules/nf-core/fq/lint/tests/main.nf.test.snap
diff --git a/modules/nf-core/fq/lint/tests/tags.yml b/modules/nf-core/fq/lint/tests/tags.yml
diff --git a/nextflow.config b/nextflow.config
@@ -82,6 +82,8 @@ params {
     unstranded_threshold       = 0.1
 
     // QC
+    skip_linting               = false
+    save_linting_log           = true
     skip_qc                    = false
     skip_bigwig                = false
     skip_stringtie             = false