s3_index_validation

nextflow run nf-core/atacseq \
    -r s3_index_validation \
    -resume \
    -profile nygc \
    --input "$SAMPLESHEET" \
    --outdir "$OUTDIR" \
    --genome GRCh38 \
    -c "${PROJECT_DIR}/epigenome_cell_lines/scripts/1-mapping/ATAC/override_igenomes.config" \
    --read_length 50 \
    --narrow_peak \
    --save_reference

The s3_index_validation branch fails on Nextflow 24.04.2 with a compilation error:


Module compilation error
- file : workflows/atacseq.nf
- cause: Variable `channel` already defined in the process scope @ line 118, column 26.
       def topic_versions = channel.topic("versions")
                            ^
The PR changed Channel (uppercase) to channel (lowercase) throughout <http://prepare_genome.nf|prepare_genome.nf> for "strict mode syntax", but workflows/atacseq.nf still uses channel as a local variable name. Nextflow 24.04.2 interprets lowercase channel as a variable reference, not the Nextflow Channel factory class, causing a name collision at line 118.

Bottom line: The branch can't even launch on Nextflow 24.04.2, so it's untestable — and separately, it still doesn't address the queue-vs-value channel root cause for BWA_MEM receiving 0 tasks

[2026-03-30 13:29:42] job START on ne1dc3-015

 N E X T F L O W   ~  version 24.04.2

WARN: Invalid config manifest attribute `contributors`
WARN: It appears you have never run this project before -- Option `-resume` is ignored
Launching `<https://github.com/nf-core/atacseq>` [trusting_wing] DSL2 - revision: e2518260cd [s3_index_validation]

WARN: Nextflow self-contained distribution allows only core plugins -- User config plugins will be ignored: nf-schema@2.5.1
WARN: Invalid config manifest attribute `contributors`
ERROR ~ Module compilation error
- file : /gpfs/commons/home/rmassoni/.nextflow/assets/nf-core/atacseq/./workflows/atacseq.nf
- cause: Variable `channel` already defined in the process scope @ line 118, column 26.
       def topic_versions = channel.topic("versions")
                            ^

1 error


 -- Check script '/gpfs/commons/home/rmassoni/.nextflow/assets/nf-core/atacseq/main.nf' at line: 37 or see '.nextflow.log' file for more details
[2026-03-30 13:30:28] job END

As expected — they only reverted channel back to Channel in <http://prepare_genome.nf|prepare_genome.nf>, but not in workflows/atacseq.nf where the error actually is (line 118: channel.topic("versions")).

And critically — looking at the BWA index section, the revert still shows:


ch_bwa_index = BWA_INDEX ( ch_fasta.map { item -> [ [:], item ] } ).index
No .collect() or .first() — the queue/value channel bug is still there.

Tell them:

Two issues with the latest commit (e251826):

Compilation still fails — workflows/atacseq.nf line 118 still has lowercase channel.topic("versions"). The revert only hit <http://prepare_genome.nf|prepare_genome.nf> but not <http://atacseq.nf|atacseq.nf>.

The original bug is still unfixed — the BWA index path when building from scratch (BWA_INDEX(...).index) is still a queue channel with no .collect() or .first(). Even if the compilation error is resolved, BWA_MEM will still receive 0 tasks.

module load Nextflow/25.10.0

executor >  slurm (45)
[cb/639c94] NFC…GENOME:GTF2BED (genes.gtf) | 1 of 1 ✔
[4c/4040ab] NFC…PREPARE_GENOME:TSS_EXTRACT | 1 of 1 ✔
[c7/7a66b1] NFC…_GETCHROMSIZES (genome.fa) | 1 of 1 ✔
[3f/72c7c0] NFC…_AUTOSOMES (genome.fa.fai) | 1 of 1 ✔
[1b/bc06c7] NFC…_REGIONS (genome.fa.sizes) | 1 of 1 ✔
[49/175f61] NFC…NOME:BWA_INDEX (genome.fa) | 1 of 1 ✔
[63/7e1891] NFC…ECK (atac_samplesheet.csv) | 1 of 1 ✔
[3e/f6c83e] NFC…:FASTQC (U-RT1_WT_REP2_T1) | 18 of 18 ✔
[e8/1a9fe5] NFC…MGALORE (U-RT1_WT_REP3_T1) | 18 of 18 ✔
[-        ] NFC…EQ:FASTQ_ALIGN_BWA:BWA_MEM -
[-        ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT -
[-        ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX -
[-        ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS -
[-        ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT -
[-        ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS -
[-        ] NFC…CARD_MERGESAMFILES_LIBRARY -
[-        ] NFC…CARD:PICARD_MARKDUPLICATES -
[-        ] NFC…ATES_PICARD:SAMTOOLS_INDEX -
[-        ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS -
[-        ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT -
[cb/c7965f] NFCORE_ATACSEQ:ATACSEQ:IGV     | 1 of 1 ✔
[64/2ae3cd] NFCORE_ATACSEQ:ATACSEQ:MULTIQC | 1 of 1 ✔
Plus 51 more processes waiting for tasks…
-[nf-core/atacseq] Pipeline completed successfully-
Completed at: 31-Mar-2026 22:18:52
Duration    : 1h 9m 1s
CPU hours   : 1.6
Succeeded   : 45