From f4ad2d07e234fa028ef35744ed988f3c44cc5f87 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 19 Sep 2023 13:37:03 -0400
Subject: [PATCH] refactor: always call fromPath with checkIfExists: true

---
 main.nf                     | 16 +++++++++-------
 subworkflows/local/peaks.nf |  6 ++----
 subworkflows/local/qc.nf    |  7 ++++---
 3 files changed, 15 insertions(+), 14 deletions(-)

diff --git a/main.nf b/main.nf
index f43c524e..b46f4024 100644
--- a/main.nf
+++ b/main.nf
@@ -37,17 +37,19 @@ workflow {
     INPUT_CHECK.out.reads.set { raw_fastqs }
     raw_fastqs | TRIM_SE
     TRIM_SE.out.set{ trimmed_fastqs }
-    blacklist_files = Channel
-                        .fromPath(params.genomes[ params.genome ].blacklist_files)
-                        .collect()
+
+    Channel.fromPath(params.genomes[ params.genome ].blacklist_files, checkIfExists: true)
+        .collect()
+        .set{ blacklist_files }
     ALIGN_BLACKLIST(trimmed_fastqs, blacklist_files)
-    reference_files = Channel
-                        .fromPath(params.genomes[ params.genome ].reference_files)
-                        .collect()
+    Channel.fromPath(params.genomes[ params.genome ].reference_files, checkIfExists: true)
+        .collect()
+        .set{ reference_files }
     ALIGN_GENOME(ALIGN_BLACKLIST.out.reads, reference_files)
     ALIGN_GENOME.out.bam.set{ aligned_bam }
 
-    chrom_sizes = Channel.fromPath(params.genomes[ params.genome ].chrom_sizes)
+    Channel.fromPath(params.genomes[ params.genome ].chrom_sizes, checkIfExists: true)
+        .set{ chrom_sizes }
     aligned_bam.combine(chrom_sizes) | DEDUPLICATE
     DEDUPLICATE.out.bam.set{ deduped_bam }
     DEDUPLICATE.out.tag_align.set{ deduped_tagalign }
diff --git a/subworkflows/local/peaks.nf b/subworkflows/local/peaks.nf
index e3ef4fa3..04759788 100644
--- a/subworkflows/local/peaks.nf
+++ b/subworkflows/local/peaks.nf
@@ -32,13 +32,11 @@ workflow CALL_PEAKS {
                 meta1, tag1, meta2, tag2 ->
                     meta1.control == meta2.id ? [ meta1, tag1, tag2 ]: null
             }
-            .combine(Channel.fromPath(params.gem_read_dists))
+            .combine(Channel.fromPath(params.gem_read_dists, checkIfExists: true))
             .combine(chrom_sizes)
             .set { ch_gem }
-        println "chr dir ${params.genomes[ params.genome ].chromosomes_dir}"
-        Channel.fromPath("${params.genomes[ params.genome ].chromosomes_dir}", type: 'dir')
+        Channel.fromPath("${params.genomes[ params.genome ].chromosomes_dir}", type: 'dir', checkIfExists: true)
             .set{ chrom_files }
-        chrom_files.view()
 
         ch_tagalign | MACS_BROAD
         ch_tagalign | MACS_NARROW
diff --git a/subworkflows/local/qc.nf b/subworkflows/local/qc.nf
index 4a79fd46..946a8aea 100644
--- a/subworkflows/local/qc.nf
+++ b/subworkflows/local/qc.nf
@@ -80,8 +80,9 @@ workflow QC {
                     meta1.control == meta2.id ? [ meta1, [ bam1, bam2 ], [ bai1, bai2 ] ] : null
             }
             .set { ch_ip_ctrl_bam_bai }
-        PLOT_FINGERPRINT(ch_ip_ctrl_bam_bai)
-        BED_PROTEIN_CODING(Channel.fromPath(params.genomes[ params.genome ].gene_info))
+        ch_ip_ctrl_bam_bai | PLOT_FINGERPRINT
+        Channel.fromPath(params.genomes[ params.genome ].gene_info,
+                         checkIfExists: true) | BED_PROTEIN_CODING
         COMPUTE_MATRIX(bigwig_list,
                        BED_PROTEIN_CODING.out.bed.combine(Channel.from('metagene','TSS'))
         )
@@ -101,7 +102,7 @@ workflow QC {
             .set { ch_ip_ctrl_bigwig }
 
         MULTIQC(
-            Channel.fromPath(params.multiqc_config),
+            Channel.fromPath(params.multiqc_config, checkIfExists: true),
             FASTQC_RAW.out.zip.collect(),
             FASTQC_TRIMMED.out.zip.collect(),
             FASTQ_SCREEN.out.screen.collect(),