diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml index 491f7bf09896046a772a366a2c69e1da1b1082c8..18a9a8b038a9a60c7b78e1b6a0cbe9a5717674f6 100644 --- a/astrocyte_pkg.yml +++ b/astrocyte_pkg.yml @@ -245,13 +245,13 @@ workflow_parameters: description: | --tss_bed. Path to BED file containing transcription start sites. This will be created from the gene BED file if not specified. -# - id: macs_gsize -# type: real -# required: false -# description: | -# --macs_gsize. parameter required by MACS2. If using an iGenomes reference these have been provided when `--genome` is set as -# *GRCh37*, *GRCh38*, *GRCm38*, *WBcel235*, *BDGP6*, *R64-1-1*, *EF2*, *hg38*, *hg19* and *mm10*. Otherwise the gsize -# will default to GRCh38. [default: 2700000000.0] + - id: macs_gsize + type: real + required: false + description: | + --macs_gsize. parameter required by MACS2. If using an iGenomes reference these have been provided when `--genome` is set as + *GRCh37*, *GRCh38*, *GRCm38*, *WBcel235*, *BDGP6*, *R64-1-1*, *EF2*, *hg38*, *hg19* and *mm10*. Otherwise the gsize + will default to GRCh38. [default: 2700000000.0] - id: blacklist type: string diff --git a/workflow/main.nf b/workflow/main.nf index 8324af8e92d49aa5d12603172638ab1aff523c13..53f50ccf33a6d9c340ac8957a54c1b57174ab435 100644 --- a/workflow/main.nf +++ b/workflow/main.nf @@ -50,7 +50,7 @@ workflow { def avail_parameters = [ "source_entrypoint", "profile", "input", "fragment_size", "read_length", "with_control", "outdir", "multiqc_title", - "genome", "fasta", "gtf", "gff", "bwa_index", "bowtie2_index", "chromap_index", "gene_bed", "tss_bed", + "genome", "fasta", "gtf", "gff", "bwa_index", "bowtie2_index", "chromap_index", "gene_bed", "tss_bed", "macs_gsize", "blacklist", "mito_name", "keep_mito", "ataqv_mito_reference", "clip_r1", "clip_r2", "three_prime_clip_r1", "three_prime_clip_r2", "trim_nextseq", "min_trimmed_reads", "skip_trimming", "aligner", "keep_dups", "keep_multi_map", "skip_merge_replicates", "narrow_peak", "broad_cutoff", "macs_fdr", "macs_pvalue", "min_reps_consensus", "skip_peak_qc", diff --git a/workflow/modules.nf b/workflow/modules.nf index 25a294076e49a8103dc3a336f245aaa40996034b..58a890f436962cda3d92e00729f1edbe26fcfdb0 100644 --- a/workflow/modules.nf +++ b/workflow/modules.nf @@ -26,6 +26,7 @@ process DEBUG_INFO { printf '%-30s : %s\n' "chromap_index" "${params.chromap_index}" printf '%-30s : %s\n' "gene_bed" "${params.gene_bed}" printf '%-30s : %s\n' "tss_bed" "${params.tss_bed}" + printf '%-30s : %s\n' "macs_gsize" "${params.macs_gsize}" printf '%-30s : %s\n' "blacklist" "${params.blacklist}" printf '%-30s : %s\n' "mito_name" "${params.mito_name}" printf '%-30s : %s\n' "keep_mito" "${params.keep_mito}"