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Bump versions to 3.18.0 #1474

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Dec 19, 2024
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Bump versions to 3.18.0 #1474

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859cfc3
Bump versions to 3.18.0
pinin4fjords Dec 19, 2024
f41744e
Update CHANGELOG.md
pinin4fjords Dec 19, 2024
492efe9
Revert "Update CHANGELOG.md"
pinin4fjords Dec 19, 2024
0cf9100
Update changelog
pinin4fjords Dec 19, 2024
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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -333,7 +333,7 @@ manifest {
description = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control."""
mainScript = 'main.nf'
nextflowVersion = '!>=24.04.2'
version = '3.18.0dev'
version = '3.18.0'
doi = 'https://doi.org/10.5281/zenodo.1400710'
}

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4 changes: 2 additions & 2 deletions tests/default.nf.test.snap
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Expand Up @@ -46,7 +46,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.18.0dev"
"nf-core/rnaseq": "v3.18.0"
}
},
[
Expand Down Expand Up @@ -240,7 +240,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.18.0dev"
"nf-core/rnaseq": "v3.18.0"
}
},
[
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4 changes: 2 additions & 2 deletions tests/featurecounts_group_type.nf.test.snap
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Expand Up @@ -46,7 +46,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.18.0dev"
"nf-core/rnaseq": "v3.18.0"
}
},
[
Expand Down Expand Up @@ -234,7 +234,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.18.0dev"
"nf-core/rnaseq": "v3.18.0"
}
},
[
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4 changes: 2 additions & 2 deletions tests/hisat2.nf.test.snap
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Expand Up @@ -47,7 +47,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.18.0dev"
"nf-core/rnaseq": "v3.18.0"
}
},
[
Expand Down Expand Up @@ -237,7 +237,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.18.0dev"
"nf-core/rnaseq": "v3.18.0"
}
},
[
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4 changes: 2 additions & 2 deletions tests/kallisto.nf.test.snap
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Expand Up @@ -59,7 +59,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.18.0dev"
"nf-core/rnaseq": "v3.18.0"
}
},
[
Expand Down Expand Up @@ -319,7 +319,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.18.0dev"
"nf-core/rnaseq": "v3.18.0"
}
},
[
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4 changes: 2 additions & 2 deletions tests/min_mapped_reads.nf.test.snap
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Expand Up @@ -137,7 +137,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.18.0dev"
"nf-core/rnaseq": "v3.18.0"
}
},
[
Expand Down Expand Up @@ -1246,7 +1246,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.18.0dev"
"nf-core/rnaseq": "v3.18.0"
}
},
[
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4 changes: 2 additions & 2 deletions tests/remove_ribo_rna.nf.test.snap
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Expand Up @@ -143,7 +143,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.18.0dev"
"nf-core/rnaseq": "v3.18.0"
}
},
[
Expand Down Expand Up @@ -1460,7 +1460,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.18.0dev"
"nf-core/rnaseq": "v3.18.0"
}
},
[
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4 changes: 2 additions & 2 deletions tests/salmon.nf.test.snap
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Expand Up @@ -53,7 +53,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.18.0dev"
"nf-core/rnaseq": "v3.18.0"
}
},
[
Expand Down Expand Up @@ -392,7 +392,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.18.0dev"
"nf-core/rnaseq": "v3.18.0"
}
},
[
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4 changes: 2 additions & 2 deletions tests/skip_qc.nf.test.snap
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Expand Up @@ -43,7 +43,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.18.0dev"
"nf-core/rnaseq": "v3.18.0"
}
},
[
Expand Down Expand Up @@ -182,7 +182,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.18.0dev"
"nf-core/rnaseq": "v3.18.0"
}
},
[
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2 changes: 1 addition & 1 deletion tests/skip_trimming.nf.test.snap
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Expand Up @@ -133,7 +133,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.18.0dev"
"nf-core/rnaseq": "v3.18.0"
}
},
[
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4 changes: 2 additions & 2 deletions tests/star_rsem.nf.test.snap
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Expand Up @@ -137,7 +137,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.18.0dev"
"nf-core/rnaseq": "v3.18.0"
}
},
[
Expand Down Expand Up @@ -1339,7 +1339,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.18.0dev"
"nf-core/rnaseq": "v3.18.0"
}
},
[
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6 changes: 3 additions & 3 deletions tests/umi.nf.test.snap
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Expand Up @@ -140,7 +140,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.18.0dev"
"nf-core/rnaseq": "v3.18.0"
}
},
[
Expand Down Expand Up @@ -1610,7 +1610,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.18.0dev"
"nf-core/rnaseq": "v3.18.0"
}
},
[
Expand Down Expand Up @@ -2747,7 +2747,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.18.0dev"
"nf-core/rnaseq": "v3.18.0"
}
},
[
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31 changes: 24 additions & 7 deletions workflows/rnaseq/assets/multiqc/multiqc_config.yml
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@@ -1,5 +1,8 @@
report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/rnaseq/tree/dev" target="_blank">nf-core/rnaseq</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/rnaseq/dev/docs/output" target="_blank">documentation</a>.
This report has been generated by the <a href="https://github.com/nf-core/rnaseq/releases/tag/3.18.0"
target="_blank">nf-core/rnaseq</a> analysis pipeline. For information about how
to interpret these results, please see the <a href="https://nf-co.re/rnaseq/3.18.0/docs/output"
target="_blank">documentation</a>.
report_section_order:
# Important checks and failures
sample-status:
Expand Down Expand Up @@ -117,9 +120,9 @@ module_order:
# Don't show % Dups in the General Stats table (we have this from Picard)
table_columns_visible:
"FastQC (raw)":
percent_duplicates: False
percent_duplicates: false
"FastQC (trimmed)":
percent_duplicates: False
percent_duplicates: false

extra_fn_clean_exts:
- ".umi_dedup"
Expand Down Expand Up @@ -216,31 +219,45 @@ sp:
custom_data:
fail_trimmed_samples:
section_name: "WARNING: Fail Trimming Check"
description: "List of samples that failed the minimum trimmed reads threshold specified via the '--min_trimmed_reads' parameter, and hence were ignored for the downstream processing steps."
description: "List of samples that failed the minimum trimmed reads threshold
specified via the '--min_trimmed_reads' parameter, and hence were ignored for
the downstream processing steps."
plot_type: "table"
pconfig:
id: "fail_trimmed_samples_table"
title: "Samples failed trimming threshold"
namespace: "Samples failed trimming threshold"
fail_mapped_samples:
section_name: "WARNING: Fail Alignment Check"
description: "List of samples that failed the STAR minimum mapped reads threshold specified via the '--min_mapped_reads' parameter, and hence were ignored for the downstream processing steps."
description: "List of samples that failed the STAR minimum mapped reads threshold
specified via the '--min_mapped_reads' parameter, and hence were ignored for
the downstream processing steps."
plot_type: "table"
pconfig:
id: "fail_mapped_samples_table"
title: "Samples failed mapping threshold"
namespace: "Samples failed mapping threshold"
fail_strand_check:
section_name: "Strandedness Checks"
description: "<p>The strandedness used for analysis in this workflow can either be provided by the user or automatically inferred by <b>Salmon</b> using a sample of reads. In both cases, strandedness is verified at the end of the workflow using <b>RSeQC</b>'s <a href='http://rseqc.sourceforge.net/#infer-experiment-py'>infer_experiment.py</a> on genomic alignments. In this table, a pass indicates a match between the supplied strandedness (or that inferred by Salmon) and RSeQC results. A fail indicates a mismatch or 'undetermined' strandedness. 'Undetermined' strandedness can signal QC issues, including potential genomic DNA contamination.</p><p><b>Note:</b> Rows are duplicated for an 'auto' setting to allow comparison of statistics between inference methods.</p>"
description: "<p>The strandedness used for analysis in this workflow can either
be provided by the user or automatically inferred by <b>Salmon</b> using a sample
of reads. In both cases, strandedness is verified at the end of the workflow
using <b>RSeQC</b>'s <a href='http://rseqc.sourceforge.net/#infer-experiment-py'>infer_experiment.py</a>
on genomic alignments. In this table, a pass indicates a match between the supplied
strandedness (or that inferred by Salmon) and RSeQC results. A fail indicates
a mismatch or 'undetermined' strandedness. 'Undetermined' strandedness can signal
QC issues, including potential genomic DNA contamination.</p><p><b>Note:</b>
Rows are duplicated for an 'auto' setting to allow comparison of statistics
between inference methods.</p>"
plot_type: "table"
pconfig:
id: "fail_strand_check_table"
title: "Samples strandedness check"
namespace: "Samples strandedness check"
headers:
Status:
description: Pass if the strandedness inferred by RSeQC matches that provided by the user or predicted by Salmon. Fail otherwise.
description: Pass if the strandedness inferred by RSeQC matches that provided
by the user or predicted by Salmon. Fail otherwise.
Strand inference method:
description: Tool used to detect strandedness
Provided strandedness:
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