Update 3 files

- /astrocyte_pkg.yml
- /workflow/main.nf
- /workflow/modules.nf

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

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",

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}"