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Add minimum_alignment_q_score parameter for MAPQ filtering (similar to nf-core/cutandrun)

enhancement

Status: Open.

#463 In nf-core/chipseq;

· wanisajad opened on May 16, 2025

JSON schema: Chipseq

docsDocumentationDocumentation

Status: Open.

#458 In nf-core/chipseq;

· jen-reeve opened on Mar 25, 2025

Call peak without chip-seq input control.

enhancement

Status: Open.

#457 In nf-core/chipseq;

· ljw20180420 opened on Mar 21, 2025

Make skip_preseq the default option

enhancement

Status: Open.

#456 In nf-core/chipseq;

· JoseEspinosa opened on Mar 13, 2025

 ·  

2.2

Make skip_preseq the default option

enhancement

Status: Open.

#455 In nf-core/chipseq;

· JoseEspinosa opened on Mar 13, 2025

Enable the use of CSI bam index

enhancement

Status: Open.

#454 In nf-core/chipseq;

· JoseEspinosa opened on Mar 12, 2025

 ·  

2.2

Can we do chip seq analysis using nextflow without input sample?

enhancement

Status: Open.

#452 In nf-core/chipseq;

· autumnfe79 opened on Mar 6, 2025

Output .bed file not found in the MACS2 folder

Status: Open.

#448 In nf-core/chipseq;

· GopishankarThirumoorthy opened on Feb 3, 2025

Container hash mismatch at <code>NFCORE_CHIPSEQ:CHIPSEQ:PHANTOMPEAKQUALTOOLS (1)</code> step

Status: Open.

#442 In nf-core/chipseq;

· alextruong opened on Dec 19, 2024

Adjust x-axis to start at 1 for custom phantompeakqualtools NSC plot

enhancement

Status: Open.

#441 In nf-core/chipseq;

· pontushojer opened on Dec 17, 2024

Add check for sample name collision when using the same sample for multiple antibodies

Status: Open.

#440 In nf-core/chipseq;

· pontushojer opened on Dec 16, 2024

Process <code>NFCORE_CHIPSEQ:CHIPSEQ:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (SRR5627136_REP2_T1)</code> terminated with an error exit status (1)

bugSomething isn't workingSomething isn't working

Status: Open.

#431 In nf-core/chipseq;

· NicoleChant opened on Oct 22, 2024