search

nf-core / atacseq

ATAC-seq peak-calling and QC analysis pipeline
https://nf-co.re/atacseq
MIT License
190 stars 118 forks source link

Latest version still generated MACS2, not MACS3 #389

Open liuyang2006 opened 3 weeks ago

liuyang2006 commented 3 weeks ago

Description of the bug

Hi,

I want to ask why I use latesest version, but my results is still macs2, not macs3.

Here is my command line:

nextflow run nf-core/atacseq -resume -c nextflow.config --input /project/sli68423_1316/users/yang/workspace/nanome/related_proje
ct/aml_nanopore/atac/00samplesheet_atac.csv --outdir results_mll_atac_hg38 -profile singularity --genome GRCh38 --read_length 50 -
-narrow_peak

Here is output directory:

ls bwa/merged_library/
ataqv                           D3_REP1.mLb.clN.sorted.bam      D6_REP1.mLb.clN.sorted.bam      deeptools
bigwig                          D3_REP1.mLb.clN.sorted.bam.bai  D6_REP1.mLb.clN.sorted.bam.bai  macs2
D1_REP1.mLb.clN.sorted.bam      D4_REP1.mLb.clN.sorted.bam      D7_REP1.mLb.clN.sorted.bam      picard_metrics
D1_REP1.mLb.clN.sorted.bam.bai  D4_REP1.mLb.clN.sorted.bam.bai  D7_REP1.mLb.clN.sorted.bam.bai  samtools_stats
D2_REP1.mLb.clN.sorted.bam      D5_REP1.mLb.clN.sorted.bam      D8_REP1.mLb.clN.sorted.bam
D2_REP1.mLb.clN.sorted.bam.bai  D5_REP1.mLb.clN.sorted.bam.bai  D8_REP1.mLb.clN.sorted.bam.bai

Command used and terminal output

nextflow run nf-core/atacseq -resume -c nextflow.config --input /project/sli68423_1316/users/yang/workspace/nanome/related_proje ct/aml_nanopore/atac/00samplesheet_atac.csv --outdir results_mll_atac_hg38 -profile singularity --genome GRCh38 --read_length 50 - -narrow_peak

Relevant files

No response

System information

No response

liuyang2006 commented 3 weeks ago

When I use dev version pipeline, it asks me to add --fasta, and --gtf options, how to fix this?

Here is my command:

nextflow run nf-core/atacseq -r dev -resume -c nextflow.config --input /project/sli68423_1316/users/yang/workspace/nanome/related_project/aml_nanopore/atac/00samplesheet_atac.csv --outdir results_mll_atac_hg38 -profile singularity --genome GRCh38 --read_length 50 --narrow_peak --fasta /project/sli68423_1316/users/yang/reference/ucsc/hg38/hg38.fa.bgz

Error message:

ERROR ~ Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* --fasta (/project/sli68423_1316/users/yang/reference/ucsc/hg38/hg38.fa.bgz): "/project/sli68423_1316/users/yang/reference/ucsc/hg38/hg38.fa.bgz" does not match regular expression [^\S+\.fn?a(sta)?(\.gz)?$]