refactor: Move uniqmap generation to references

nf-core/references#3
nf-core · Nov 16, 2024 · f1d2b5a · f1d2b5a
1 parent cb95feb
commit f1d2b5a
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Showing 5 changed files with 22 additions and 32 deletions.
diff --git a/main.nf b/main.nf
@@ -69,6 +69,7 @@ workflow NFCORE_NASCENT {
         params.bowtie2_index,
         params.hisat2_index,
         params.star_index,
+        params.homer_uniqmap
     )
     emit:
     multiqc_report = NASCENT.out.multiqc_report // channel: /path/to/multiqc_report.html

diff --git a/modules/nf-core/homer/findpeaks/main.nf b/modules/nf-core/homer/findpeaks/main.nf
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -254,6 +254,12 @@
                     "fa_icon": "fas fa-copy",
                     "help_text": "> **NB** If none provided, index will be generated automatically from the FASTA reference."
                 },
+                "homer_uniqmap": {
+                    "type": "string",
+                    "description": "Path to HOMER uniqmap file or URL to download.",
+                    "fa_icon": "fas fa-file-archive",
+                    "help_text": "> **NB** If none provided, will be downloaded automatically from the HOMER website. See nf-core/references for generation"
+                },
                 "save_reference": {
                     "type": "boolean",
                     "description": "If generated by the pipeline save the BWA index in the results directory.",

diff --git a/subworkflows/nf-core/homer/groseq/main.nf b/subworkflows/nf-core/homer/groseq/main.nf
diff --git a/workflows/nascent.nf b/workflows/nascent.nf
@@ -59,6 +59,7 @@ workflow NASCENT {
     ch_bowtie2_index
     ch_hisat2_index
     ch_star_index
+    ch_uniqmap
 
 
     main:
@@ -294,6 +295,7 @@ workflow NASCENT {
         ch_gxf,
         PREPARE_GENOME.out.fasta,
         PREPARE_GENOME.out.chrom_sizes,
+        ch_uniqmap
     )
     ch_grohmm_multiqc = TRANSCRIPT_INDENTIFICATION.out.grohmm_td_plot.collect()
     ch_homer_multiqc = TRANSCRIPT_INDENTIFICATION.out.homer_peaks