Merge branch 'dev' into fix-de-tutorial

Author: mashehu

.github/workflows/ci.yml

@@ -51,7 +51,6 @@ jobs:
       matrix:
         NXF_VER:
           - "24.04.2"
-          - "latest-everything"
         nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"]
         profile:
           - "docker"

CHANGELOG.md

@@ -3,19 +3,52 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-# 3.18.0dev - xxxx-xx-xx
+# 3.19.0dev - xxxx-xx-xx
+
+### Credits
+
+### Enhancements & fixes
+
+- [PR #1480](https://github.com/nf-core/rnaseq/pull/1480) - Bump version after release 3.18.0
+- [PR #1482](https://github.com/nf-core/rnaseq/pull/1482) - Update trimgalore module for save_unpaired fix
+- [PR #1486](https://github.com/nf-core/rnaseq/pull/1486) - Bump STAR build for multiprocessing fix
+- [PR #1490](https://github.com/nf-core/rnaseq/pull/1490) - Make genomic FASTA input optional
+
+# 3.18.0 - 2024-12-19
 
 ### Credits
 
 Special thanks to the following for their contributions to the release:
 
 - [Caitlin Winkler](https://github.com/oligomyeggo)
+- [Jonathan Manning](https://github.com/pinin4fjords)
+- [Lorenzo Sola](https://github.com/LorenzoS96)
+- [Maxime Garcia](https://github.com/maxulysse)
 - [Siddhartha Bagaria](https://github.com/siddharthab)
 
 ### Enhancements & fixes
 
 - [PR #1369](https://github.com/nf-core/rnaseq/pull/1369) - Add umicollapse as an alternative to umi-tools
 - [PR #1461](https://github.com/nf-core/rnaseq/pull/1461) - Add FASTQ linting during preprocessing
+- [PR #1463](https://github.com/nf-core/rnaseq/pull/1463) - Move channel operations outside of the onComplete() block
+- [PR #1467](https://github.com/nf-core/rnaseq/pull/1467) - Add test suite for UMI handling functionality
+- [PR #1466](https://github.com/nf-core/rnaseq/pull/1466) - Factor out UMI handling
+- [PR #1470](https://github.com/nf-core/rnaseq/pull/1470) - Update subworkflow to account for fix to bad argument handling
+- [PR #1469](https://github.com/nf-core/rnaseq/pull/1469) - Minor docs fix
+- [PR #1459](https://github.com/nf-core/rnaseq/pull/1466) - Remove reference to unused "skip_sample_count" value in email templates
+- [PR #1471](https://github.com/nf-core/rnaseq/pull/1471) - Fix prepare_genome subworkflow for sortmerna
+- [PR #1473](https://github.com/nf-core/rnaseq/pull/1473) - Bump STAR modules
+- [PR #1474](https://github.com/nf-core/rnaseq/pull/1474) - Bump versions to 3.18.0
+- [PR #1475](https://github.com/nf-core/rnaseq/pull/1475) - Fix log publishing around umitools/ umicollapse
+- [PR #1447](https://github.com/nf-core/rnaseq/pull/1447) - Add tutorial series for analysing count data
+
+## Parameters
+
+| Old parameter | New parameter         |
+| ------------- | --------------------- |
+|               | `--skip_linting`      |
+|               | `--extra_fqlint_args` |
+|               | `--umi_dedup_tool`    |
 
 ### Software dependencies
 

assets/email_template.html

@@ -34,25 +34,6 @@ <h4 style="margin-top: 0; color: inherit">nf-core/rnaseq execution completed uns
         <p>The full error message was:</p>
         <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0">${errorReport}</pre>
       </div>
-      """ } else if(skip_sample_count > 0) { out << """
-      <div
-        style="
-          color: #856404;
-          background-color: #fff3cd;
-          border-color: #ffeeba;
-          padding: 15px;
-          margin-bottom: 20px;
-          border: 1px solid transparent;
-          border-radius: 4px;
-        "
-      >
-        <h4 style="margin-top: 0; color: inherit">nf-core/rnaseq execution completed with warnings!</h4>
-        <p>
-          The pipeline finished successfully, but samples were skipped. Please check warnings at the top of the MultiQC report.
-        </p>
-        <p></p>
-      </div>
-
       """ } else { out << """
       <div
         style="

assets/email_template.txt

@@ -17,13 +17,6 @@ The full error message was:
 
 ${errorReport}
 """
-} else if (skip_sample_count > 0) {
-    out << """##################################################
-## nf-core/rnaseq execution completed with warnings ##
-##################################################
-The pipeline finished successfully, but samples were skipped.
-Please check warnings at the top of the MultiQC report.
-"""
 } else {
     out << "## nf-core/rnaseq execution completed successfully! ##"
 }

bin/filter_gtf.py

@@ -6,7 +6,7 @@
 import argparse
 import re
 import statistics
-from typing import Set
+from typing import Optional, Set
 
 # Create a logger
 logging.basicConfig(format="%(name)s - %(asctime)s %(levelname)s: %(message)s")
@@ -27,14 +27,15 @@ def tab_delimited(file: str) -> float:
         return statistics.median(line.count("\t") for line in data.split("\n"))
 
 
-def filter_gtf(fasta: str, gtf_in: str, filtered_gtf_out: str, skip_transcript_id_check: bool) -> None:
+def filter_gtf(fasta: Optional[str], gtf_in: str, filtered_gtf_out: str, skip_transcript_id_check: bool) -> None:
     """Filter GTF file based on FASTA sequence names."""
     if tab_delimited(gtf_in) != 8:
         raise ValueError("Invalid GTF file: Expected 9 tab-separated columns.")
 
-    seq_names_in_genome = extract_fasta_seq_names(fasta)
-    logger.info(f"Extracted chromosome sequence names from {fasta}")
-    logger.debug("All sequence IDs from FASTA: " + ", ".join(sorted(seq_names_in_genome)))
+    if (fasta is not None):
+        seq_names_in_genome = extract_fasta_seq_names(fasta)
+        logger.info(f"Extracted chromosome sequence names from {fasta}")
+        logger.debug("All sequence IDs from FASTA: " + ", ".join(sorted(seq_names_in_genome)))
 
     seq_names_in_gtf = set()
     try:
@@ -44,7 +45,7 @@ def filter_gtf(fasta: str, gtf_in: str, filtered_gtf_out: str, skip_transcript_i
                 seq_name = line.split("\t")[0]
                 seq_names_in_gtf.add(seq_name)  # Add sequence name to the set
 
-                if seq_name in seq_names_in_genome:
+                if fasta is None or seq_name in seq_names_in_genome:
                     if skip_transcript_id_check or re.search(r'transcript_id "([^"]+)"', line):
                         out.write(line)
                         line_count += 1
@@ -63,7 +64,7 @@ def filter_gtf(fasta: str, gtf_in: str, filtered_gtf_out: str, skip_transcript_i
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description="Filters a GTF file based on sequence names in a FASTA file.")
     parser.add_argument("--gtf", type=str, required=True, help="GTF file")
-    parser.add_argument("--fasta", type=str, required=True, help="Genome fasta file")
+    parser.add_argument("--fasta", type=str, required=False, help="Genome fasta file")
     parser.add_argument("--prefix", dest="prefix", default="genes", type=str, help="Prefix for output GTF files")
     parser.add_argument(
         "--skip_transcript_id_check", action="store_true", help="Skip checking for transcript IDs in the GTF file"

conf/arm.config

@@ -121,11 +121,11 @@ process {
     }
 
     withName: 'STAR_GENOMEGENERATE' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a2/a2d5226e4ce3dee8b29154c16a87d282d96c76e75b6678d032643902591586e2/data' : 'community.wave.seqera.io/library/htslib_samtools_star_gawk:1d1b7da208684cac' }
+        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/40/40d803371e50330de0773c7cc50315e2c3b4b41dcf123823adeb0a07d71654c1/data' : 'community.wave.seqera.io/library/htslib_samtools_star_gawk:ae438e9a604351a4' }
     }
 
     withName: 'STAR_ALIGN' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a2/a2d5226e4ce3dee8b29154c16a87d282d96c76e75b6678d032643902591586e2/data' : 'community.wave.seqera.io/library/htslib_samtools_star_gawk:1d1b7da208684cac' }
+        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/40/40d803371e50330de0773c7cc50315e2c3b4b41dcf123823adeb0a07d71654c1/data' : 'community.wave.seqera.io/library/htslib_samtools_star_gawk:ae438e9a604351a4' }
     }
 
     withName: 'TXIMETA_TXIMPORT' {

docs/images/mqc_fastqc_adapter.png

@@ -74,7 +74,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 If multiple libraries/runs have been provided for the same sample in the input samplesheet (e.g. to increase sequencing depth) then these will be merged at the very beginning of the pipeline in order to have consistent sample naming throughout the pipeline. Please refer to the [usage documentation](https://nf-co.re/rnaseq/usage#samplesheet-input) to see how to specify these samples in the input samplesheet.
 
-# fq lint
+### fq lint
 
 <details markdown="1">
 <summary>Output files</summary>
@@ -120,7 +120,7 @@ If multiple libraries/runs have been provided for the same sample in the input s
 
 </details>
 
-[UMI-tools](https://github.com/CGATOxford/UMI-tools) deduplicates reads based on unique molecular identifiers (UMIs) to address PCR-bias. Firstly, the UMI-tools `extract` command removes the UMI barcode information from the read sequence and adds it to the read name. Secondly, reads are deduplicated based on UMI identifier after mapping as highlighted in the [UMI-tools dedup](#umi-tools-dedup) section.
+[UMI-tools](https://github.com/CGATOxford/UMI-tools) and [UMICollapse](https://github.com/Daniel-Liu-c0deb0t/UMICollapse) deduplicate reads based on unique molecular identifiers (UMIs) to address PCR-bias. Firstly, the UMI-tools `extract` command removes the UMI barcode information from the read sequence and adds it to the read name. Secondly, reads are deduplicated based on UMI identifier after mapping as highlighted in the [UMI dedup](#umi-dedup) section.
 
 To facilitate processing of input data which has the UMI barcode already embedded in the read name from the start, `--skip_umi_extract` can be specified in conjunction with `--with_umi`.
 
@@ -305,7 +305,7 @@ The original BAM files generated by the selected alignment algorithm are further
 
 ![MultiQC - SAMtools mapped reads per contig plot](images/mqc_samtools_idxstats.png)
 
-### UMI-tools dedup
+### UMI dedup
 
 <details markdown="1">
 <summary>Output files</summary>
@@ -314,7 +314,7 @@ The original BAM files generated by the selected alignment algorithm are further
   - `<SAMPLE>.umi_dedup.sorted.bam`: If `--save_umi_intermeds` is specified the UMI deduplicated, coordinate sorted BAM file containing read alignments will be placed in this directory.
   - `<SAMPLE>.umi_dedup.sorted.bam.bai`: If `--save_umi_intermeds` is specified the BAI index file for the UMI deduplicated, coordinate sorted BAM file will be placed in this directory.
   - `<SAMPLE>.umi_dedup.sorted.bam.csi`: If `--save_umi_intermeds --bam_csi_index` is specified the CSI index file for the UMI deduplicated, coordinate sorted BAM file will be placed in this directory.
-- `<ALIGNER>/umitools/`
+- `<ALIGNER>/umitools/` (UMI-tools only)
   - `*_edit_distance.tsv`: Reports the (binned) average edit distance between the UMIs at each position.
   - `*_per_umi.tsv`: UMI-level summary statistics.
   - `*_per_umi_per_position.tsv`: Tabulates the counts for unique combinations of UMI and position.
@@ -323,7 +323,7 @@ The content of the files above is explained in more detail in the [UMI-tools doc
 
 </details>
 
-After extracting the UMI information from the read sequence (see [UMI-tools extract](#umi-tools-extract)), the second step in the removal of UMI barcodes involves deduplicating the reads based on both mapping and UMI barcode information using the UMI-tools `dedup` command. This will generate a filtered BAM file after the removal of PCR duplicates.
+After extracting the UMI information from the read sequence (see [UMI-tools extract](#umi-tools-extract)), the second step in the removal of UMI barcodes involves deduplicating the reads based on both mapping and UMI barcode information. UMI deduplication can be carried out either with [UMI-tools](https://github.com/CGATOxford/UMI-tools) or [UMICollapse](https://github.com/Daniel-Liu-c0deb0t/UMICollapse), set via the `umi_dedup_tool` parameter. The output BAM files are the same, though UMI-tools has some additional outputs, as described above. Either method will generate a filtered BAM file after the removal of PCR duplicates.
 
 ### picard MarkDuplicates