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Merged
maxulysse merged 10 commits into from
Dec 12, 2025
Merged

Sample naming fixes #121

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48ec9d5
group paired samples in tables (fix #105)
pontushojer Jul 9, 2025
4eb9dd0
remove suffix added by fastqscreen
pontushojer Jul 9, 2025
205ae76
use sample name for prefix
pontushojer Jul 9, 2025
abfa1c8
revert 205ae76b329903f52373f91344f954ba586d8570 and update sample nam…
pontushojer Aug 8, 2025
80a1bf8
prettify naming in report while distinguishing between assigned index…
pontushojer Aug 8, 2025
d026acd
cleanups
pontushojer Oct 7, 2025
ffc9b87
update changelog
pontushojer Oct 7, 2025
69e4948
update snapshots
pontushojer Oct 7, 2025
70dd2ae
Merge branch 'dev' into sample-naming
maxulysse Dec 12, 2025
b3e0da0
re-generate snapshots
maxulysse Dec 12, 2025
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5 changes: 3 additions & 2 deletions CHANGELOG.md
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Expand Up @@ -26,13 +26,13 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
- [#86](https://github.com/nf-core/seqinspector/issues/86) Update lists of default steps in the pipeline
- [#84](https://github.com/nf-core/seqinspector/issues/84) Short summary of seqinspector in README.md
- [#110](https://github.com/nf-core/seqinspector/pull/110) Update input schema to accept either tar file or directory as rundir, and fastq messages and patterns.
- [#135](https://github.com/nf-core/seqinspector/pull/135) Added index section to MultiQC reports to facilitate report navigation (#125)
- [#127](https://github.com/nf-core/seqinspector/pull/127) Added alignment tools - bwamem2 - index and mem
- [#128](https://github.com/nf-core/seqinspector/pull/128) Added Picard tools - Collect Multiple Mterics to collect QC metrics
- [#132](https://github.com/nf-core/seqinspector/pull/132) Added a bwamem2 index params for faster output
- [#135](https://github.com/nf-core/seqinspector/pull/135) Added index section to MultiQC reports to facilitate report navigation (#125)
- [#151](https://github.com/nf-core/seqinspector/pull/151) Added a prepare_genome subworkflow to handle bwamem2 indexing
- [#159](https://github.com/nf-core/seqinspector/pull/159) Added a subworkflow QC_BAM including picard_collecthsmetrics for alignment QC of hybrid-selection data
- [#158](https://github.com/nf-core/seqinspector/pull/158) Moved picard_collectmultiplemetrics to the subworkflow QC_BAM
- [#159](https://github.com/nf-core/seqinspector/pull/159) Added a subworkflow QC_BAM including picard_collecthsmetrics for alignment QC of hybrid-selection data
- [#162](https://github.com/nf-core/seqinspector/pull/162) Add tests for prepare_genome subworkflow

### `Fixed`
Expand All @@ -41,6 +41,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
- [#99](https://github.com/nf-core/seqinspector/pull/99) Fix group reports for paired reads
- [#107](https://github.com/nf-core/seqinspector/pull/107) Put SeqFU-stats section reports together
- [#112](https://github.com/nf-core/seqinspector/pull/112) Making fastq_screen_references value to use parentDir
- [#121](https://github.com/nf-core/seqinspector/pull/121) Cleanup sample naming for MultiQC report (#105)
- [#94] (https://github.com/nf-core/seqinspector/issues/94) Go through and validate test data
- [#162](https://github.com/nf-core/seqinspector/pull/162) Fix bugs in qc_bam and prepare_genome subworkflows and add tests
- [#163](https://github.com/nf-core/seqinspector/pull/163) Run fastqscreen with subsampled data if available
Expand Down
19 changes: 19 additions & 0 deletions assets/multiqc_config.yml
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Expand Up @@ -15,3 +15,22 @@ report_section_order:
export_plots: true

disable_version_detection: true

fn_clean_trim:
- "_screen" # Added by FastqScreen

# Make sample name with indexes a bit prettier
# for SE: "SampleName_01" -> "SampleName #01"
# for PE: "SampleName_01_1" -> "SampleName #01_1"
# and: "SampleName_01_2" -> "SampleName #01_2"
sample_names_replace_regex: True
sample_names_replace:
"(.+)_(\\d{2,}|\\d{2,}_[12])$": "\\1 #\\2"

table_sample_merge:
"Read1":
- type: regex
pattern: "_1$"
"Read2":
- type: regex
pattern: "_2$"
6 changes: 5 additions & 1 deletion subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
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Expand Up @@ -100,6 +100,8 @@ workflow PIPELINE_INITIALISATION {
//
// Create channel from input file provided through params.input
//
nr_samples = Channel.fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
.toList().size()

channel
.fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
Expand All @@ -108,7 +110,9 @@ workflow PIPELINE_INITIALISATION {
.map {
meta, fastq_1, fastq_2, idx ->
def tags = meta.tags ? meta.tags.tokenize(":") : []
def updated_meta = meta + [ id:"${meta.sample}_${idx}", tags:tags ]
def pad_positions = [nr_samples.length(), 2].max()
def zero_padded_idx = idx.padLeft(pad_positions, "0")
def updated_meta = meta + [ id:"${meta.sample}_${zero_padded_idx}", tags:tags ]
if (!fastq_2) {
return [
updated_meta.id,
Expand Down
200 changes: 100 additions & 100 deletions tests/MiSeq.main.nf.test.snap
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254 changes: 127 additions & 127 deletions tests/MiSeq_PairedEnd.main.nf.test.snap
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562 changes: 281 additions & 281 deletions tests/NovaSeq6000.main.nf.test.snap
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582 changes: 291 additions & 291 deletions tests/NovaSeq6000.main_subsample.nf.test.snap
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62 changes: 31 additions & 31 deletions tests/PromethION.main.nf.test.snap
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Expand Up @@ -17,12 +17,12 @@
},
[
"fastqc",
"fastqc/hg001_1_fastqc.html",
"fastqc/hg001_1_fastqc.zip",
"fastqc/hg001_01_fastqc.html",
"fastqc/hg001_01_fastqc.zip",
"fastqscreen",
"fastqscreen/hg001_1_screen.html",
"fastqscreen/hg001_1_screen.png",
"fastqscreen/hg001_1_screen.txt",
"fastqscreen/hg001_01_screen.html",
"fastqscreen/hg001_01_screen.png",
"fastqscreen/hg001_01_screen.txt",
"multiqc",
"multiqc/global_report",
"multiqc/global_report/multiqc_data",
Expand All @@ -47,7 +47,7 @@
"multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
"multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
"multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
"multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
"multiqc/global_report/multiqc_data/multiqc_seqfu_mqc.txt",
"multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
"multiqc/global_report/multiqc_data/multiqc_sources.txt",
"multiqc/global_report/multiqc_plots",
Expand All @@ -66,7 +66,7 @@
"multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
"multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
"multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
"multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
"multiqc/global_report/multiqc_plots/pdf/seqfu_mqc.pdf",
"multiqc/global_report/multiqc_plots/png",
"multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
"multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
Expand All @@ -82,7 +82,7 @@
"multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
"multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
"multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
"multiqc/global_report/multiqc_plots/png/seqfu.png",
"multiqc/global_report/multiqc_plots/png/seqfu_mqc.png",
"multiqc/global_report/multiqc_plots/svg",
"multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
"multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
Expand All @@ -98,46 +98,46 @@
"multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
"multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
"multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
"multiqc/global_report/multiqc_plots/svg/seqfu.svg",
"multiqc/global_report/multiqc_plots/svg/seqfu_mqc.svg",
"multiqc/global_report/multiqc_report.html",
"pipeline_info",
"pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
"samtools_faidx",
"samtools_faidx/genome.fa.fai",
"samtools_faidx/genome.fa.sizes",
"seqfu_stats",
"seqfu_stats/hg001_1_seqfu.tsv",
"seqfu_stats/hg001_1_seqfu_mqc.txt"
"seqfu_stats/hg001_01_seqfu.tsv",
"seqfu_stats/hg001_01_seqfu_mqc.txt"
],
[
"hg001_1_screen.png:md5,b9c58e388f18ad11f4c2e29e9b573a5e",
"hg001_1_screen.txt:md5,8e53ea043d658a130f4b8ca455e2ba9b",
"fastq_screen_plot.txt:md5,3023b86477fecf6d46d8fc60d82cc53a",
"fastqc-status-check-heatmap.txt:md5,825668e94de27356f0a112beb758e416",
"fastqc_adapter_content_plot.txt:md5,1fa991080c20755e5e729a5eeab960e5",
"fastqc_overrepresented_sequences_plot.txt:md5,e810a3d3eba0ba83b122763505f511a7",
"fastqc_per_base_n_content_plot.txt:md5,cbdb64298ff839665e8c8c8e89896e87",
"fastqc_per_base_sequence_quality_plot.txt:md5,4962950bc3ce77169ac510d64cb769c6",
"fastqc_per_sequence_gc_content_plot_Counts.txt:md5,e62273533304be59dab5f13afef93b3e",
"fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,3d49290a15406cb5dac1460c02729f0f",
"fastqc_per_sequence_quality_scores_plot.txt:md5,7cc10d1bc92ca09431a506c38d911228",
"fastqc_sequence_counts_plot.txt:md5,0425d7298c24df6158d5bf7aca1d4190",
"fastqc_sequence_duplication_levels_plot.txt:md5,9111d942c7eed5af0e9ccb8c42db8505",
"fastqc_sequence_length_distribution_plot.txt:md5,04adfcd0125ebcc3e3bb631f1956c812",
"hg001_01_screen.png:md5,b9c58e388f18ad11f4c2e29e9b573a5e",
"hg001_01_screen.txt:md5,8e53ea043d658a130f4b8ca455e2ba9b",
"fastq_screen_plot.txt:md5,f6883339d43a090e86e02fdf3feacbbd",
"fastqc-status-check-heatmap.txt:md5,0ac9450d210de9ab4548378101877c8e",
"fastqc_adapter_content_plot.txt:md5,6e2a760185573c44180ca43081cc7c99",
"fastqc_overrepresented_sequences_plot.txt:md5,251ad51e27e966476911ff4c77c2a893",
"fastqc_per_base_n_content_plot.txt:md5,230b2a0319f3b7490498e8edb47b17bf",
"fastqc_per_base_sequence_quality_plot.txt:md5,4934bce34aec037e1ea590bd69f74781",
"fastqc_per_sequence_gc_content_plot_Counts.txt:md5,028ada8fc060ce4af7476f339c57c50d",
"fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,6bab830c22525c15a6048d8054f685cf",
"fastqc_per_sequence_quality_scores_plot.txt:md5,fd29224ed588e37e1fc85bf7f717e31e",
"fastqc_sequence_counts_plot.txt:md5,cc83b291e21249f3c4e25d34cc898f0f",
"fastqc_sequence_duplication_levels_plot.txt:md5,7b7665c78ca66d3e13b1850701b198dc",
"fastqc_sequence_length_distribution_plot.txt:md5,d7bac93b11316846778b9d550f323371",
"multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
"multiqc_fastq_screen.txt:md5,7c5d711e27c53d13c81644a1f2468dba",
"multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0",
"multiqc_seqfu.txt:md5,9595d608ff5709f2bdec8cb1016416c0",
"multiqc_fastq_screen.txt:md5,0ab0d1c4c3e3393afdb50ad0e116e394",
"multiqc_fastqc.txt:md5,b71aaffef9767dfe9d83fde0d31a3a1b",
"multiqc_seqfu_mqc.txt:md5,9595d608ff5709f2bdec8cb1016416c0",
"genome.fa.fai:md5,59557cd3a71ca5e0840285b6088ec1d6",
"genome.fa.sizes:md5,f154a58a25ba9c4d386003eaa1bb731b",
"hg001_1_seqfu.tsv:md5,b133752c897afbb4d8721b911fa117d4",
"hg001_1_seqfu_mqc.txt:md5,42e3506b02ceb72a6f05cb174505e722"
"hg001_01_seqfu.tsv:md5,b133752c897afbb4d8721b911fa117d4",
"hg001_01_seqfu_mqc.txt:md5,42e3506b02ceb72a6f05cb174505e722"
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-12-03T11:01:17.46398"
"timestamp": "2025-12-12T10:05:23.380990836"
}
}