Skip to content

Commit dbfc744

Browse files
pinin4fjordspinin4fjords
authored
Merge branch 'dev' into allow_int_samplenames
2 parents fc78482 + bdd52ec commit dbfc744

File tree

247 files changed

+12420
-4403
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

247 files changed

+12420
-4403
lines changed

‎.github/workflows/ci.yml‎

Lines changed: 7 additions & 38 deletions
Original file line numberDiff line numberDiff line change
@@ -54,41 +54,25 @@ jobs:
5454
- "latest-everything"
5555
nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"]
5656
profile:
57-
- "conda"
5857
- "docker"
5958
- "singularity"
6059
isMaster:
6160
- ${{ github.base_ref == 'master' }}
6261
# Exclude conda and singularity on dev
6362
exclude:
6463
- isMaster: false
65-
profile: "conda"
66-
- isMaster: false
6764
profile: "singularity"
68-
- profile: "conda"
69-
nf_test_files: "tests/default.nf.test"
70-
- profile: "conda"
71-
nf_test_files: "tests/featurecounts_group_type.nf.test"
72-
- profile: "conda"
73-
nf_test_files: "tests/hisat2.nf.test"
74-
- profile: "conda"
75-
nf_test_files: "tests/kallisto.nf.test"
76-
- profile: "conda"
77-
nf_test_files: "tests/min_mapped_reads.nf.test"
78-
- profile: "conda"
79-
nf_test_files: "tests/remove_ribo_rna.nf.test"
80-
- profile: "conda"
81-
nf_test_files: "tests/salmon.nf.test"
82-
- profile: "conda"
83-
nf_test_files: "tests/skip_qc.nf.test"
84-
- profile: "conda"
85-
nf_test_files: "tests/skip_trimming.nf.test"
86-
- profile: "conda"
87-
nf_test_files: "tests/star_rsem.nf.test"
65+
- NXF_VER: "latest-everything"
66+
profile: "singularity"
8867
steps:
8968
- name: Check out pipeline code
9069
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
9170

71+
- uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
72+
with:
73+
distribution: "temurin"
74+
java-version: "17"
75+
9276
- name: Set up Nextflow
9377
uses: nf-core/setup-nextflow@v2
9478
with:
@@ -104,21 +88,6 @@ jobs:
10488
mkdir -p $NXF_SINGULARITY_CACHEDIR
10589
mkdir -p $NXF_SINGULARITY_LIBRARYDIR
10690
107-
- name: Set up Miniconda
108-
if: matrix.profile == 'conda'
109-
uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
110-
with:
111-
miniconda-version: "latest"
112-
auto-update-conda: true
113-
conda-solver: libmamba
114-
channels: conda-forge,bioconda
115-
116-
- name: Set up Conda
117-
if: matrix.profile == 'conda'
118-
run: |
119-
echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
120-
echo $(realpath python) >> $GITHUB_PATH
121-
12291
- name: Install nf-test
12392
uses: nf-core/setup-nf-test@v1
12493
with:

‎CHANGELOG.md‎

Lines changed: 142 additions & 30 deletions
Original file line numberDiff line numberDiff line change
@@ -3,6 +3,118 @@
33
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
44
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
55

6+
# 3.19.0dev - xxxx-xx-xx
7+
8+
### Credits
9+
10+
### Enhancements & fixes
11+
12+
- [PR #1480](https://github.com/nf-core/rnaseq/pull/1480) - Bump version after release 3.18.0
13+
- [PR #1482](https://github.com/nf-core/rnaseq/pull/1482) - Update trimgalore module for save_unpaired fix
14+
- [pR #1486](https://github.com/nf-core/rnaseq/pull/1486) - Bump STAR build for multiprocessing fix
15+
16+
# 3.18.0 - 2024-12-19
17+
18+
### Credits
19+
20+
Special thanks to the following for their contributions to the release:
21+
22+
- [Caitlin Winkler](https://github.com/oligomyeggo)
23+
- [Jonathan Manning](https://github.com/pinin4fjords)
24+
- [Lorenzo Sola](https://github.com/LorenzoS96)
25+
- [Maxime Garcia](https://github.com/maxulysse)
26+
- [Siddhartha Bagaria](https://github.com/siddharthab)
27+
28+
### Enhancements & fixes
29+
30+
- [PR #1369](https://github.com/nf-core/rnaseq/pull/1369) - Add umicollapse as an alternative to umi-tools
31+
- [PR #1461](https://github.com/nf-core/rnaseq/pull/1461) - Add FASTQ linting during preprocessing
32+
- [PR #1463](https://github.com/nf-core/rnaseq/pull/1463) - Move channel operations outside of the onComplete() block
33+
- [PR #1467](https://github.com/nf-core/rnaseq/pull/1467) - Add test suite for UMI handling functionality
34+
- [PR #1466](https://github.com/nf-core/rnaseq/pull/1466) - Factor out UMI handling
35+
- [PR #1470](https://github.com/nf-core/rnaseq/pull/1470) - Update subworkflow to account for fix to bad argument handling
36+
- [PR #1469](https://github.com/nf-core/rnaseq/pull/1469) - Minor docs fix
37+
- [PR #1459](https://github.com/nf-core/rnaseq/pull/1466) - Remove reference to unused "skip_sample_count" value in email templates
38+
- [PR #1471](https://github.com/nf-core/rnaseq/pull/1471) - Fix prepare_genome subworkflow for sortmerna
39+
- [PR #1473](https://github.com/nf-core/rnaseq/pull/1473) - Bump STAR modules
40+
- [PR #1474](https://github.com/nf-core/rnaseq/pull/1474) - Bump versions to 3.18.0
41+
- [PR #1475](https://github.com/nf-core/rnaseq/pull/1475) - Fix log publishing around umitools/ umicollapse
42+
- [PR #1447](https://github.com/nf-core/rnaseq/pull/1447) - Add tutorial series for analysing count data
43+
44+
## Parameters
45+
46+
| Old parameter | New parameter |
47+
| ------------- | --------------------- |
48+
| | `--skip_linting` |
49+
| | `--extra_fqlint_args` |
50+
| | `--umi_dedup_tool` |
51+
52+
### Software dependencies
53+
54+
| Dependency | Old version | New version |
55+
| ------------- | ----------- | ----------- |
56+
| `UMICollapse` | | 1.1.0 |
57+
58+
> **NB:** Dependency has been **updated** if both old and new version information is present.
59+
>
60+
> **NB:** Dependency has been **added** if just the new version information is present.
61+
>
62+
> **NB:** Dependency has been **removed** if new version information isn't present.
63+
64+
## [[3.17.0](https://github.com/nf-core/rnaseq/releases/tag/3.17.0)] - 2024-10-23
65+
66+
### Credits
67+
68+
Special thanks to the following for their contributions to the release:
69+
70+
- [Maxime Garcia](https://github.com/maxulysse)
71+
- [Jonathan Manning](https://github.com/pinin4fjords)
72+
- [Pablo Gonzalez de Aledo](https://github.com/pabloaledo)
73+
74+
### Enhancements & fixes
75+
76+
- [PR #1418](https://github.com/nf-core/rnaseq/pull/1418) - Bump versions back to 3.17.0 after release
77+
- [PR #1422](https://github.com/nf-core/rnaseq/pull/1422) - Bump lots of modules so that conda versions have ARM builds
78+
- [PR #1423](https://github.com/nf-core/rnaseq/pull/1423) - Bump STAR version for version with ARM Conda build
79+
- [PR #1424](https://github.com/nf-core/rnaseq/pull/1424) - Patch sortmerna to 4.3.7 for ARM compatibility
80+
- [PR #1425](https://github.com/nf-core/rnaseq/pull/1425) - Add profile for ARM compatibility
81+
- [PR #1432](https://github.com/nf-core/rnaseq/pull/1432) - Bump versions for 3.17.0 release
82+
- [PR #1434](https://github.com/nf-core/rnaseq/pull/1434) - Default registry is quay.io for all containers
83+
- [PR #1437](https://github.com/nf-core/rnaseq/pull/1437) - Update software dependencies
84+
- [PR #1437](https://github.com/nf-core/rnaseq/pull/1437) - Remove conda from test matrix
85+
- [PR #1440](https://github.com/nf-core/rnaseq/pull/1440) - Further reduce matrix
86+
- [PR #1441](https://github.com/nf-core/rnaseq/pull/1441) - Force some containers to be converted from docker to singularity to fix nf-core download tests
87+
88+
### Software dependencies
89+
90+
| Dependency | Old version | New version |
91+
| ----------------------------- | ----------- | ----------- |
92+
| `bbmap` | 39.01 | 39.10 |
93+
| `coreutils` | 8.30 | 9.5 |
94+
| `fq` | 0.9.1 | 0.12.0 |
95+
| `python (catadditionalfasta)` | 3.9.5 | 3.12.2 |
96+
| `python (tx2gene)` | 3.9.5 | 3.10.4 |
97+
| `cutadapt` | 3.4 | 4.9 |
98+
| `htslib (star)` | 1.18 | 1.20 |
99+
| `htslib` | 1.20 | 1.21 |
100+
| `kallisto` | 0.48.0 | 0.51.1 |
101+
| `preseq` | 3.1.2 | 3.2.0 |
102+
| `salmon` | 1.10.1 | 1.10.3 |
103+
| `samtools (star)` | 1.18 | 1.20 |
104+
| `samtools` | 1.20 | 1.21 |
105+
| `sortmerna` | 4.3.6 | 4.3.7 |
106+
| `star` | 2.7.10a | =2.7.11b |
107+
| `stringtie` | 2.2.1 | 2.2.3 |
108+
| `subread` | 2.0.1 | 2.0.6 |
109+
| `trim-galore` | 0.6.7 | 0.6.10 |
110+
| `ucsc-bedgraphtobigwig` | 445 | 469 |
111+
112+
> **NB:** Dependency has been **updated** if both old and new version information is present.
113+
>
114+
> **NB:** Dependency has been **added** if just the new version information is present.
115+
>
116+
> **NB:** Dependency has been **removed** if new version information isn't present.
117+
6118
## [[3.16.1](https://github.com/nf-core/rnaseq/releases/tag/3.16.1)] - 2024-10-16
7119

8120
### Credits
@@ -953,14 +1065,14 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
9531065

9541066
### Parameters
9551067

956-
| Old parameter | New parameter |
957-
| --------------------------- | -------------------------------------- |
958-
| `--fc_extra_attributes` | `--gtf_extra_attributes` |
959-
|  `--fc_group_features` |  `--gtf_group_features` |
960-
|  `--fc_count_type` |  `--gtf_count_type` |
961-
|  `--fc_group_features_type` |  `--gtf_group_features_type` |
962-
|   |  `--singularity_pull_docker_container` |
963-
|  `--skip_featurecounts` |   |
1068+
| Old parameter | New parameter |
1069+
| -------------------------- | ------------------------------------- |
1070+
| `--fc_extra_attributes` | `--gtf_extra_attributes` |
1071+
| `--fc_group_features` | `--gtf_group_features` |
1072+
| `--fc_count_type` | `--gtf_count_type` |
1073+
| `--fc_group_features_type` | `--gtf_group_features_type` |
1074+
| | `--singularity_pull_docker_container` |
1075+
| `--skip_featurecounts` | |
9641076

9651077
> **NB:** Parameter has been **updated** if both old and new parameter information is present.
9661078
> **NB:** Parameter has been **added** if just the new parameter information is present.
@@ -1038,28 +1150,28 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
10381150

10391151
#### Updated
10401152

1041-
| Old parameter | New parameter |
1042-
| ----------------------------- | --------------------------- |
1043-
| `--reads` | `--input` |
1044-
|  `--igenomesIgnore` |  `--igenomes_ignore` |
1045-
|  `--removeRiboRNA` |  `--remove_ribo_rna` |
1046-
|  `--rRNA_database_manifest` |  `--ribo_database_manifest` |
1047-
|  `--save_nonrRNA_reads` |  `--save_non_ribo_reads` |
1048-
|  `--saveAlignedIntermediates` |  `--save_align_intermeds` |
1049-
|  `--saveReference` |  `--save_reference` |
1050-
|  `--saveTrimmed` |  `--save_trimmed` |
1051-
|  `--saveUnaligned` |  `--save_unaligned` |
1052-
|  `--skipAlignment` |  `--skip_alignment` |
1053-
|  `--skipBiotypeQC` |  `--skip_biotype_qc` |
1054-
|  `--skipDupRadar` |  `--skip_dupradar` |
1055-
|  `--skipFastQC` |  `--skip_fastqc` |
1056-
|  `--skipMultiQC` |  `--skip_multiqc` |
1057-
|  `--skipPreseq` |  `--skip_preseq` |
1058-
|  `--skipQC` |  `--skip_qc` |
1059-
|  `--skipQualimap` |  `--skip_qualimap` |
1060-
|  `--skipRseQC` |  `--skip_rseqc` |
1061-
|  `--skipTrimming` |  `--skip_trimming` |
1062-
|  `--stringTieIgnoreGTF` |  `--stringtie_ignore_gtf` |
1153+
| Old parameter | New parameter |
1154+
| ---------------------------- | -------------------------- |
1155+
| `--reads` | `--input` |
1156+
| `--igenomesIgnore` | `--igenomes_ignore` |
1157+
| `--removeRiboRNA` | `--remove_ribo_rna` |
1158+
| `--rRNA_database_manifest` | `--ribo_database_manifest` |
1159+
| `--save_nonrRNA_reads` | `--save_non_ribo_reads` |
1160+
| `--saveAlignedIntermediates` | `--save_align_intermeds` |
1161+
| `--saveReference` | `--save_reference` |
1162+
| `--saveTrimmed` | `--save_trimmed` |
1163+
| `--saveUnaligned` | `--save_unaligned` |
1164+
| `--skipAlignment` | `--skip_alignment` |
1165+
| `--skipBiotypeQC` | `--skip_biotype_qc` |
1166+
| `--skipDupRadar` | `--skip_dupradar` |
1167+
| `--skipFastQC` | `--skip_fastqc` |
1168+
| `--skipMultiQC` | `--skip_multiqc` |
1169+
| `--skipPreseq` | `--skip_preseq` |
1170+
| `--skipQC` | `--skip_qc` |
1171+
| `--skipQualimap` | `--skip_qualimap` |
1172+
| `--skipRseQC` | `--skip_rseqc` |
1173+
| `--skipTrimming` | `--skip_trimming` |
1174+
| `--stringTieIgnoreGTF` | `--stringtie_ignore_gtf` |
10631175

10641176
#### Added
10651177

‎assets/email_template.html‎

Lines changed: 0 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -34,25 +34,6 @@ <h4 style="margin-top: 0; color: inherit">nf-core/rnaseq execution completed uns
3434
<p>The full error message was:</p>
3535
<pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0">${errorReport}</pre>
3636
</div>
37-
""" } else if(skip_sample_count > 0) { out << """
38-
<div
39-
style="
40-
color: #856404;
41-
background-color: #fff3cd;
42-
border-color: #ffeeba;
43-
padding: 15px;
44-
margin-bottom: 20px;
45-
border: 1px solid transparent;
46-
border-radius: 4px;
47-
"
48-
>
49-
<h4 style="margin-top: 0; color: inherit">nf-core/rnaseq execution completed with warnings!</h4>
50-
<p>
51-
The pipeline finished successfully, but samples were skipped. Please check warnings at the top of the MultiQC report.
52-
</p>
53-
<p></p>
54-
</div>
55-
5637
""" } else { out << """
5738
<div
5839
style="

‎assets/email_template.txt‎

Lines changed: 0 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -17,13 +17,6 @@ The full error message was:
1717

1818
${errorReport}
1919
"""
20-
} else if (skip_sample_count > 0) {
21-
out << """##################################################
22-
## nf-core/rnaseq execution completed with warnings ##
23-
##################################################
24-
The pipeline finished successfully, but samples were skipped.
25-
Please check warnings at the top of the MultiQC report.
26-
"""
2720
} else {
2821
out << "## nf-core/rnaseq execution completed successfully! ##"
2922
}

0 commit comments

Comments
 (0)