From 8ad861a645e86c411b47472616a924063afba106 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Thu, 28 Apr 2022 13:52:03 +0200
Subject: [PATCH] add fasta index

---
 subworkflows/nf-core/bam_qc_picard/main.nf       | 12 +++++++-----
 subworkflows/nf-core/bam_qc_picard/meta.yml      | 10 +++++-----
 tests/subworkflows/nf-core/bam_qc_picard/main.nf | 12 +++++++-----
 3 files changed, 19 insertions(+), 15 deletions(-)

diff --git a/subworkflows/nf-core/bam_qc_picard/main.nf b/subworkflows/nf-core/bam_qc_picard/main.nf
index 9e429448..e6f82feb 100644
--- a/subworkflows/nf-core/bam_qc_picard/main.nf
+++ b/subworkflows/nf-core/bam_qc_picard/main.nf
@@ -10,14 +10,17 @@ workflow BAM_QC_PICARD {
     take:
     ch_bam              // channel: [ val(meta), [ bam ]]
     ch_fasta            // channel: [ fasta ]
+    ch_fasta_faix       // channel: [ fasta_fai ]
     ch_bait_interval    // channel: [ bait_interval ]
     ch_target_interval  // channel: [ target_interval ]
 
     main:
     ch_versions = Channel.empty()
+    ch_coverage_metrics = Channel.empty()
 
     PICARD_COLLECTMULTIPLEMETRICS( ch_bam, ch_fasta )
     ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
+
     if (ch_bait_interval || ch_target_interval) {
         if (ch_bait_interval.isEmpty()) {
             log.error("Bait interval channel is empty")
@@ -26,18 +29,17 @@ workflow BAM_QC_PICARD {
             log.error("Target interval channel is empty")
         }
         PICARD_COLLECTHSMETRICS( ch_bam, ch_fasta, [], ch_bait_interval, ch_target_interval )
+        ch_coverage_metrics.mix(PICARD_COLLECTHSMETRICS.out.coverage_metrics.first())
         ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
     } else {
         PICARD_COLLECTWGSMETRICS( ch_bam, ch_fasta )
         ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS.out.versions.first())
+        ch_coverage_metrics.mix(PICARD_COLLECTWGSMETRICS.out.coverage_metrics.first())
     }
 
-    ch_coverage_metrics = Channel.empty()
-    ch_coverage_metrics.mix(PICARD_COLLECTHSMETRICS.out.coverage_metrics.first(), PICARD_COLLECTWGSMETRICS.out.coverage_metrics.first())
-
     emit:
-    coverage_metrics    = PICARD_COLLECTWGSMETRICS.out.metrics      // channel: [ val(meta), [ coverage_metrics ] ]
+    coverage_metrics    = ch_coverage_metrics                       // channel: [ val(meta), [ coverage_metrics ] ]
     multiple_metrics    = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), [ multiple_metrics ] ]
 
-    versions = ch_versions                                          // channel: [ versions.yml ]
+    versions            = ch_versions                               // channel: [ versions.yml ]
 }
diff --git a/subworkflows/nf-core/bam_qc_picard/meta.yml b/subworkflows/nf-core/bam_qc_picard/meta.yml
index 67d3496e..c45215d1 100644
--- a/subworkflows/nf-core/bam_qc_picard/meta.yml
+++ b/subworkflows/nf-core/bam_qc_picard/meta.yml
@@ -22,14 +22,14 @@ input:
       type: file
       description: BAM/CRAM/SAM file
       pattern: "*.{bam,cram,sam}"
-  - bai:
-      type: file
-      description: Index for BAM/CRAM/SAM file
-      pattern: "*.{bai,crai,sai}"
   - fasta:
       type: optional file
-      description: Reference file the CRAM was created with
+      description: Reference fasta file
       pattern: "*.{fasta,fa}"
+  - fasta_fai:
+      type: optional file
+      description: Reference fasta file index
+      pattern: "*.{fasta,fa}.fai"
   - bait_intervals:
       type: optional file
       description: An interval list file that contains the locations of the baits used.
diff --git a/tests/subworkflows/nf-core/bam_qc_picard/main.nf b/tests/subworkflows/nf-core/bam_qc_picard/main.nf
index 03696b44..a3e2ed62 100644
--- a/tests/subworkflows/nf-core/bam_qc_picard/main.nf
+++ b/tests/subworkflows/nf-core/bam_qc_picard/main.nf
@@ -9,17 +9,19 @@ workflow test_bam_qc_picard_wgs {
                 file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
             ]
     fasta   = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fasta_fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
 
-    BAM_QC_PICARD ( input, fasta, [], [] )
+    BAM_QC_PICARD ( input, fasta, fasta_fai, [], [] )
 }
 
 workflow test_bam_qc_picard_targetted {
     input = [ [ id:'test', single_end:false ], // meta map
                 file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
             ]
-    fasta   = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    bait    = file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true)
-    target  = file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true)
+    fasta       = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fasta_fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    bait        = file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true)
+    target      = file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true)
 
-    BAM_QC_PICARD ( input, fasta, bait, target )
+    BAM_QC_PICARD ( input, fasta, fasta_fai, bait, target )
 }