Comments (3)
chuan-wang
commented on May 10, 2024
1
Hi @orzechoj, with the large refactor in PR #51, now the pipeline supports MACS peak calling for all igenome references. So we can drop this task. Hopefully you haven't spent too much time on it!
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orzechoj
commented on May 10, 2024
I have created a test data set, using public data (subsets mapping to chr22 of hg19). There are some other problems with the pipeline (issue #43), so I haven't been able to test everything yet. When this is done I'll update the test data.
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apeltzer
commented on May 10, 2024
HI @orzechoj - will update the Docker/Singularity image once my conda recipe updates are built/deployed by CircleCI on bioconda - that should make continuing for you easier!
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Related Issues (20)
- MACS2 steps did not carried out HOT 2
- Add --only_step options
- Provide replicate information explicitly in samplesheet HOT 5
- Header missing is in bowtie2 outputted bam files
- Problem with samplesheet HOT 3
- Process `NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BWA_MEM (EBAC_Input_REP2_T1)` terminated with an error exit status (1) HOT 3
- mergeBed ERROR: Requested column 10, but database file - only has fields 1 - 9. HOT 18
- Normalisation of bigwig files
- package or namespace load failed for ‘UpSetR’ HOT 3
- No Space left on device error HOT 3
- Make subworkflows & modules available for nf-core tools HOT 1
- Default values for p-value and FDR
- Get rid of checkIfExists for params paths
- minor "samplesheet_pe.csv" format issue
- PHANTOMPEAKQUALTOOLS throws stack overflow exception HOT 1
- MACS2: Too few paired peaks (0) so I can not build the model!
- Error with NextSeq trimming
- Error running the pipline test in the BWA index step
- jobs failing with sigbus and unknown userid errors HOT 1
- Update MACS to v3
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