From 50f0e7f1fb3f28b7d535e239ee4aa285ec1644d6 Mon Sep 17 00:00:00 2001
From: Achisha Saikia <achisha.saikia@utsouthwestern.edu>
Date: Fri, 24 Jan 2025 16:43:50 -0600
Subject: [PATCH] Update 3 files
- /astrocyte_pkg.yml
- /workflow/main.nf
- /workflow/modules.nf
---
astrocyte_pkg.yml | 14 +++++++-------
workflow/main.nf | 2 +-
workflow/modules.nf | 1 +
3 files changed, 9 insertions(+), 8 deletions(-)
diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index 491f7bf..18a9a8b 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 8324af8..53f50cc 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 25a2940..58a890f 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}"
--
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