delete bedtools

nf-core · Aug 19, 2024 · 480f24e · 480f24e
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -247,6 +247,7 @@ jobs:
           - tags: "gatk4spark/applybqsr"
           - tags: "gatk4spark/markduplicates"
           - tags: "gawk"
+          - tags: "lofreq"
           - tags: "mosdepth"
           - tags: "multiqc"
           - tags: "ngscheckmate/ncm"

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -28,10 +28,6 @@
 
   > Li H: A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011 Nov 1;27(21):2987-93. doi: 10.1093/bioinformatics/btr509. PubMed PMID: 21903627; PubMed Central PMCID: PMC3198575.
 
-- [Bedtools](https://pubmed.ncbi.nlm.nih.gov/20110278/)
-
-  > Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28. PMID: 20110278; PMCID: PMC2832824.
-
 - [BGZip](https://github.com/madler/pigz)
 
 - [BWA-MEM](https://arxiv.org/abs/1303.3997v2)

diff --git a/README.md b/README.md
@@ -44,7 +44,7 @@ Depending on the options and samples provided, the pipeline can currently perfor
 - Form consensus reads from UMI sequences (`fgbio`)
 - Sequencing quality control and trimming (enabled by `--trim_fastq`) (`FastQC`, `fastp`)
 - Map Reads to Reference (`BWA-mem`, `BWA-mem2`, `dragmap` or `Sentieon BWA-mem`)
-- Process BAM file (`GATK MarkDuplicates`,`bedtools`, `GATK BaseRecalibrator` and `GATK ApplyBQSR` or `Sentieon LocusCollector` and `Sentieon Dedup`)
+- Process BAM file (`GATK MarkDuplicates`, `GATK BaseRecalibrator` and `GATK ApplyBQSR` or `Sentieon LocusCollector` and `Sentieon Dedup`)
 - Summarise alignment statistics (`samtools stats`, `mosdepth`)
 - Variant calling (enabled by `--tools`, see [compatibility](https://nf-co.re/sarek/latest/docs/usage#which-variant-calling-tool-is-implemented-for-which-data-type)):
   - `ASCAT`

diff --git a/docs/output.md b/docs/output.md
@@ -21,7 +21,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
     - [BWA-mem2](#bwa-mem2)
     - [DragMap](#dragmap)
     - [Sentieon BWA mem](#sentieon-bwa-mem)
-    - [Bedtools](#bedtools)
   - [Mark Duplicates](#mark-duplicates)
     - [GATK MarkDuplicates (Spark)](#gatk-markduplicates-spark)
   - [Sentieon LocusCollector and Dedup](#sentieon-locuscollector-and-dedup)
@@ -197,21 +196,6 @@ The alignment files (BAM or CRAM) produced by the chosen aligner are not publish
   - BAM file and index
   </details>
 
-#### Bedtools
-
-[Bedtools](https://github.com/arq5x/bedtools2) utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic. Bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.
-While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.
-
-<details markdown="1">
-<summary>Output files for all samples</summary>
-
-**Output directory: `{outdir}/reports/bedtools/`**
-
-- `<sample>.bed`
-  - When applying bedtools sort to a .bed file, the lines are reordered so that the genomic regions are in ascending order according to their position in the genome.
-  - When applying bedtools merge, overlapping or adjacent regions are combined into one, reducing redundancy and creating longer intervals that cover all the original regions.
-  </details>
-
 </details>
 
 ### Mark Duplicates

diff --git a/modules.json b/modules.json
@@ -36,16 +36,6 @@
                         "git_sha": "a5ba4d59c2b248c0379b0f8aeb4e7e754566cd1f",
                         "installed_by": ["modules"]
                     },
-                    "bedtools/merge": {
-                        "branch": "master",
-                        "git_sha": "a3d614e4a7b8691a259bcfe33ad80903217d6215",
-                        "installed_by": ["modules"]
-                    },
-                    "bedtools/sort": {
-                        "branch": "master",
-                        "git_sha": "571a5feac4c9ce0a8df0bc15b94230e7f3e8db47",
-                        "installed_by": ["modules"]
-                    },
                     "bwa/index": {
                         "branch": "master",
                         "git_sha": "086fa66260595e123b0ea47a6512539b72a9afa3",

diff --git a/modules/nf-core/bedtools/merge/environment.yml b/modules/nf-core/bedtools/merge/environment.yml
diff --git a/modules/nf-core/bedtools/merge/main.nf b/modules/nf-core/bedtools/merge/main.nf
diff --git a/modules/nf-core/bedtools/merge/meta.yml b/modules/nf-core/bedtools/merge/meta.yml
diff --git a/modules/nf-core/bedtools/merge/tests/main.nf.test b/modules/nf-core/bedtools/merge/tests/main.nf.test
diff --git a/modules/nf-core/bedtools/merge/tests/main.nf.test.snap b/modules/nf-core/bedtools/merge/tests/main.nf.test.snap
diff --git a/modules/nf-core/bedtools/merge/tests/nextflow.config b/modules/nf-core/bedtools/merge/tests/nextflow.config
diff --git a/modules/nf-core/bedtools/merge/tests/tags.yml b/modules/nf-core/bedtools/merge/tests/tags.yml
diff --git a/modules/nf-core/bedtools/sort/environment.yml b/modules/nf-core/bedtools/sort/environment.yml
diff --git a/modules/nf-core/bedtools/sort/main.nf b/modules/nf-core/bedtools/sort/main.nf
diff --git a/modules/nf-core/bedtools/sort/meta.yml b/modules/nf-core/bedtools/sort/meta.yml