| Parameter | Value |
|---|
| cores | 8 |
| ram | 30 |
| scratch | 100 |
| partition | user |
| process_mode | DATASET |
| samples | S1_undiff,S2_undiff,S3_undiff,S4_diff,S5_diff,S6_diff |
| nfcorePipeline | chipseq |
| pipelineVersion | 2.1.0 |
| inputType | samplesheet |
| samplesheetMapping | {"sample":"Name","fastq_1":"Read1 [File]","fastq_2":"Read2 [File]","replicate":"Replicate","antibody":"Antibody","control":"Control"} |
| fasta | /srv/GT/reference/Homo_sapiens/GENCODE/GRCh38.p14/Sequence/WholeGenomeFasta/genome.fa |
| fragment_size | 200 |
| seq_center | |
| read_length | 50 |
| multiqc_title | |
| genome | |
| gtf | |
| gff | |
| bwa_index | |
| bowtie2_index | |
| chromap_index | |
| star_index | |
| gene_bed | |
| macs_gsize | |
| blacklist | |
| save_reference | false |
| clip_r1 | 2 |
| clip_r2 | 2 |
| three_prime_clip_r1 | 0 |
| three_prime_clip_r2 | 0 |
| trim_nextseq | 0 |
| skip_trimming | false |
| save_trimmed | false |
| aligner | bwa |
| keep_dups | false |
| keep_multi_map | false |
| bwa_min_score | 0 |
| save_align_intermeds | false |
| save_unaligned | false |
| narrow_peak | false |
| broad_cutoff | 0.1 |
| macs_fdr | |
| macs_pvalue | |
| min_reps_consensus | 1 |
| save_macs_pileup | false |
| skip_peak_qc | false |
| skip_peak_annotation | false |
| skip_consensus_peaks | false |
| skip_fastqc | false |
| skip_picard_metrics | false |
| skip_preseq | false |
| deseq2_vst | true |
| skip_plot_profile | false |
| skip_plot_fingerprint | false |
| skip_spp | false |
| skip_deseq2_qc | false |
| skip_igv | false |
| skip_multiqc | false |
| skip_qc | false |
| sushi_app | NfCoreChipseqApp |
| refBuild | Homo_sapiens/GENCODE/GRCh38.p14/Annotation/Release_48-2025-07-03 |
