nf-core chipseq issues - Githubissues

nf-core / chipseq

ChIP-seq peak-calling, QC and differential analysis pipeline.

https://nf-co.re/chipseq

MIT License

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issues

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Fix GFFREAD

#435 ftabaro opened 4 days ago
1
Prevent pipeline fails from erroneous param validation when igenomes is used

#434 JoseEspinosa closed 4 days ago
1
Prevent pipeline fails from erroneous param validation when igenomes is used

#433 JoseEspinosa closed 4 days ago
2
Process `NFCORE_CHIPSEQ:PREPARE_GENOME:GFFREAD` declares 2 input channels but 1 were specified

#432 ftabaro opened 5 days ago
0
Process `NFCORE_CHIPSEQ:CHIPSEQ:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (SRR5627136_REP2_T1)` terminated with an error exit status (1)

#431 NicoleChant opened 1 month ago
0
Trimgalore nextseq correction

#430 cmatKhan closed 1 month ago
2
cutadapt `trim_nextseq` config typo

#429 cmatKhan closed 1 month ago
1
Process `NFCORE_CHIPSEQ:CHIPSEQ:MULTIQC` terminated with an error exit status

#428 Sungryong-Oh opened 1 month ago
0
Not a valid path value when provide genome by fasta and gtf in compressed gz format, and not providing genome index or gene bed

#427 ljw20180420 opened 1 month ago
1
Merging template 3.0.2

#426 JoseEspinosa closed 1 month ago
1
Important! Template update for nf-core/tools v3.0.2

#425 nf-core-bot closed 1 month ago
0
Merging-template-3.0.1

#424 JoseEspinosa closed 1 month ago
1
Bump version 2.2.0dev

#423 JoseEspinosa closed 1 month ago
1
Important! Template update for nf-core/tools v3.0.1

#422 nf-core-bot closed 1 month ago
1
Important! Template update for nf-core/tools v3.0.0

#421 nf-core-bot closed 1 month ago
1
Fix how replicates are set for downstream analysis

#420 JoseEspinosa closed 1 month ago
1
Fix how replicates are set for downstream analysis

#419 JoseEspinosa closed 1 month ago
1
Apply review suggestions

#418 JoseEspinosa closed 1 month ago
1
Refactor local modules to use an conda environment yml file and not ping modules directly

#417 JoseEspinosa opened 1 month ago
0
Move the KHMER_UNIQUEKMERS logic to prepare_genome

#416 JoseEspinosa opened 1 month ago
0
Get rid of oras from module images

#415 JoseEspinosa closed 1 month ago
1
Permission denied at the beginning of the pipeline

#414 paolamaragno closed 2 months ago
0
Dev -> Master for 2.1.0 release

#413 JoseEspinosa closed 1 month ago
1
Dev -> Master for 2.1.0 release

#412 JoseEspinosa closed 2 months ago
2
Error: Process `NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BOWTIE2:BOWTIE2_ALIGN (WT_HA_IP_REP1_T1)` terminated with an error exit status (1)

#411 Sungryong-Oh closed 3 months ago
1
Bulk update of modules and subworkflows for 2.1.0 release

#410 JoseEspinosa closed 3 months ago
1
Update modules and subworkflows for 2.1.0 release

#409 JoseEspinosa closed 3 months ago
2
Several fixes

#408 JoseEspinosa closed 3 months ago
1
Always upload logs when running aws full tests

#407 JoseEspinosa closed 4 months ago
2
Update images to macs3

#406 JoseEspinosa closed 4 months ago
1
Add read group tag to bowtie2 bams

#405 JoseEspinosa closed 4 months ago
1
Switch from macs2 to macs3

#404 JoseEspinosa closed 4 months ago
1
Get rid of checksamplesheet.py and switch to nf-schema

#403 JoseEspinosa opened 4 months ago
0
Clean up and removal of double slashes

#402 bjlang closed 4 months ago
2
create subworkflows/local/bam_peaks_call_qc_annotate_macs2_homer similar to nf-core/atacseq

#401 bjlang closed 4 months ago
1
use subworkflows/local/bam_peaks_call_qc_annotate_macs2_homer from nf-core/atacseq

#400 bjlang closed 4 months ago
1
use subworkflows/local/bam_bedgraph_bigwig_bedtools_ucsc from nf-core…

#399 bjlang closed 4 months ago
2
Streamline nf-core/chipseq and nf-core/atacseq by using shared subworkflows

#398 bjlang closed 4 months ago
0
Check for sample IDs characters in samplesheet

#397 JoseEspinosa closed 4 months ago
1
The "sample" field from the samplesheet is too lenient

#396 JoseEspinosa closed 4 months ago
1
Fix save_unaligned parameter description in schema

#395 JoseEspinosa closed 4 months ago
1
Fix save_unaligned parameter description in schema

#394 JoseEspinosa closed 4 months ago
1
Merge template version 2.14.1

#393 JoseEspinosa closed 4 months ago
2
check: Adding line number to error messages.

#392 smoe closed 4 months ago
2
Get rid of lib to merge tools v2.14.1

#391 JoseEspinosa closed 4 months ago
1
Important! Template update for nf-core/tools v2.14.1

#390 nf-core-bot closed 4 months ago
0
Important! Template update for nf-core/tools v2.14.0

#389 nf-core-bot closed 6 months ago
1
Macs2 Output

#388 kittyBS closed 3 months ago
2
Remove lib folder to get ready for v2.13.1 template merge

#387 JoseEspinosa closed 4 months ago
1
IDR analysis

#386 ZeinBader closed 4 months ago
2