feat: fastaidx -> fai (#1073)

modules/gatk4/applybqsr/main.nf

@@ -21,7 +21,7 @@ process GATK4_APPLYBQSR {
     input:
     tuple val(meta), path(input), path(input_index), path(bqsr_table)
     path  fasta
-    path  fastaidx
+    path  fai
     path  dict
     path  intervals
 

modules/gatk4/applybqsr/meta.yml

@@ -34,12 +34,15 @@ input:
   - fasta:
       type: file
       description: The reference fasta file
-  - fastaidx:
+      pattern: "*.fasta"
+  - fai:
       type: file
       description: Index of reference fasta file
+      pattern: "*.fasta.fai"
   - dict:
       type: file
       description: GATK sequence dictionary
+      pattern: "*.dict"
   - intervalsBed:
       type: file
       description: Bed file with the genomic regions included in the library (optional)

modules/gatk4/baserecalibrator/main.nf

@@ -21,7 +21,7 @@ process GATK4_BASERECALIBRATOR {
     input:
     tuple val(meta), path(input), path(input_index)
     path fasta
-    path fastaidx
+    path fai
     path dict
     path intervalsBed
     path knownSites

modules/gatk4/baserecalibrator/meta.yml

@@ -31,12 +31,15 @@ input:
   - fasta:
       type: file
       description: The reference fasta file
-  - fastaidx:
+      pattern: "*.fasta"
+  - fai:
       type: file
       description: Index of reference fasta file
+      pattern: "*.fasta.fai"
   - dict:
       type: file
       description: GATK sequence dictionary
+      pattern: "*.dict"
   - intervalsBed:
       type: file
       description: Bed file with the genomic regions included in the library (optional)

modules/gatk4/createsomaticpanelofnormals/main.nf

@@ -21,7 +21,7 @@ process GATK4_CREATESOMATICPANELOFNORMALS {
     input:
     tuple val(meta), path(genomicsdb)
     path fasta
-    path fastaidx
+    path fai
     path dict
 
     output:

modules/gatk4/createsomaticpanelofnormals/meta.yml

@@ -28,10 +28,10 @@ input:
       type: file
       description: The reference fasta file
       pattern: "*.fasta"
-  - fastaidx:
+  - fai:
       type: file
       description: Index of reference fasta file
-      pattern: "fasta.fai"
+      pattern: "*.fasta.fai"
   - dict:
       type: file
       description: GATK sequence dictionary

modules/gatk4/filtermutectcalls/main.nf

@@ -21,7 +21,7 @@ process GATK4_FILTERMUTECTCALLS {
     input:
     tuple val(meta), path(vcf), path(tbi), path(stats), path(orientationbias), path(segmentation), path(contaminationfile), val(contaminationest)
     path fasta
-    path fastaidx
+    path fai
     path dict
 
     output:

modules/gatk4/filtermutectcalls/meta.yml

@@ -53,10 +53,10 @@ input:
       type: file
       description: The reference fasta file
       pattern: "*.fasta"
-  - fastaidx:
+  - fai:
       type: file
       description: Index of reference fasta file
-      pattern: "fasta.fai"
+      pattern: "*.fasta.fai"
   - dict:
       type: file
       description: GATK sequence dictionary

modules/gatk4/mutect2/main.nf

@@ -25,7 +25,7 @@ process GATK4_MUTECT2 {
     val  run_mito
     val  interval_label
     path fasta
-    path fastaidx
+    path fai
     path dict
     path germline_resource
     path germline_resource_tbi

modules/gatk4/mutect2/meta.yml

@@ -54,10 +54,10 @@ input:
       type: file
       description: The reference fasta file
       pattern: "*.fasta"
-  - fastaidx:
+  - fai:
       type: file
       description: Index of reference fasta file
-      pattern: "fasta.fai"
+      pattern: "*.fasta.fai"
   - dict:
       type: file
       description: GATK sequence dictionary

subworkflows/nf-core/gatk_create_som_pon/main.nf

@@ -14,7 +14,7 @@ workflow GATK_CREATE_SOM_PON {
     take:
     ch_mutect2_in       // channel: [ val(meta), [ input ], [ input_index ], [] ]
     fasta               // channel: /path/to/reference/fasta
-    fastaidx            // channel: /path/to/reference/fasta/index
+    fai                 // channel: /path/to/reference/fasta/index
     dict                // channel: /path/to/reference/fasta/dictionary
     pon_name            // channel: name for panel of normals
     interval_file       // channel: /path/to/interval/file
@@ -25,7 +25,7 @@ workflow GATK_CREATE_SOM_PON {
     //
     //Perform variant calling for each sample using mutect2 module in panel of normals mode.
     //
-    GATK4_MUTECT2 ( input , false , true, false , [] , fasta , fastaidx , dict , [], [] , [] , [] )
+    GATK4_MUTECT2 ( input, false, true, false, [], fasta, fai, dict, [], [], [], [] )
     ch_versions = ch_versions.mix(GATK4_MUTECT2.out.versions.first())
 
     //
@@ -41,7 +41,7 @@ workflow GATK_CREATE_SOM_PON {
     //Panel of normals made from genomicsdb workspace using createsomaticpanelofnormals.
     //
     GATK4_GENOMICSDBIMPORT.out.genomicsdb.view()
-    GATK4_CREATESOMATICPANELOFNORMALS ( GATK4_GENOMICSDBIMPORT.out.genomicsdb, fasta, fastaidx, dict )
+    GATK4_CREATESOMATICPANELOFNORMALS ( GATK4_GENOMICSDBIMPORT.out.genomicsdb, fasta, fai, dict )
     ch_versions = ch_versions.mix(GATK4_CREATESOMATICPANELOFNORMALS.out.versions.first())
 
     emit:

subworkflows/nf-core/gatk_create_som_pon/meta.yml

@@ -30,10 +30,10 @@ input:
       type: file
       description: The reference fasta file
       pattern: "*.fasta"
-  - fastaidx:
+  - fai:
       type: file
       description: Index of reference fasta file
-      pattern: "fasta.fai"
+      pattern: "*.fasta.fai"
   - dict:
       type: file
       description: GATK sequence dictionary

tests/modules/gatk4/filtermutectcalls/main.nf

@@ -6,7 +6,7 @@ include { GATK4_FILTERMUTECTCALLS } from '../../../../modules/gatk4/filtermutect
 
 workflow test_gatk4_filtermutectcalls_base {
 
-    input = [ 
+    input = [
         [ id:'test'], // meta map
         file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
         file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_tbi'], checkIfExists: true),
@@ -18,15 +18,15 @@ workflow test_gatk4_filtermutectcalls_base {
     ]
 
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
     dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
 
-    GATK4_FILTERMUTECTCALLS ( input, fasta, fastaidx, dict )
+    GATK4_FILTERMUTECTCALLS ( input, fasta, fai, dict )
 }
 
 workflow test_gatk4_filtermutectcalls_with_files {
 
-    input = [ 
+    input = [
         [ id:'test'], // meta map
         file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
         file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_tbi'], checkIfExists: true),
@@ -38,15 +38,15 @@ workflow test_gatk4_filtermutectcalls_with_files {
     ]
 
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
     dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
 
-    GATK4_FILTERMUTECTCALLS ( input, fasta, fastaidx, dict )
+    GATK4_FILTERMUTECTCALLS ( input, fasta, fai, dict )
 }
 
 workflow test_gatk4_filtermutectcalls_use_val {
 
-    input = [ 
+    input = [
         [ id:'test'], // meta map
         file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
         file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_tbi'], checkIfExists: true),
@@ -58,8 +58,8 @@ workflow test_gatk4_filtermutectcalls_use_val {
     ]
 
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
     dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
 
-    GATK4_FILTERMUTECTCALLS ( input, fasta, fastaidx, dict )
+    GATK4_FILTERMUTECTCALLS ( input, fasta, fai, dict )
 }

tests/modules/gatk4/mutect2/main.nf

@@ -8,8 +8,8 @@ include { GATK4_MUTECT2 as GATK4_TEMPFIX_MUTECT2 } from '../../../../modules/gat
 
 workflow test_gatk4_mutect2_tumor_normal_pair {
     input = [ [ id:'test'], // meta map
-              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true) , file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)],
+              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)],
-              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true) , file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)],
+              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)],
               ["testN"]
             ]
     run_single = false
@@ -17,14 +17,14 @@ workflow test_gatk4_mutect2_tumor_normal_pair {
     run_mito = false
     interval_label = []
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
     dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
     germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true)
     germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true)
     panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz'], checkIfExists: true)
     panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz_tbi'], checkIfExists: true)
 
-    GATK4_TEMPFIX_MUTECT2 ( input , run_single , run_pon , run_mito , interval_label , fasta , fastaidx , dict , germline_resource, germline_resource_tbi , panel_of_normals , panel_of_normals_tbi )
+    GATK4_TEMPFIX_MUTECT2 ( input, run_single, run_pon, run_mito, interval_label, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
 }
 
 workflow test_gatk4_mutect2_tumor_single {
@@ -38,14 +38,14 @@ workflow test_gatk4_mutect2_tumor_single {
     run_mito = false
     interval_label = []
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
     dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
     germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true)
     germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true)
     panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz'], checkIfExists: true)
     panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz_tbi'], checkIfExists: true)
 
-    GATK4_MUTECT2 ( input , run_single , run_pon , run_mito , interval_label , fasta , fastaidx , dict , germline_resource, germline_resource_tbi , panel_of_normals , panel_of_normals_tbi )
+    GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, interval_label, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
 }
 
 workflow test_gatk4_mutect2_cram_input {
@@ -59,14 +59,14 @@ workflow test_gatk4_mutect2_cram_input {
     run_mito = false
     interval_label = []
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
     dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
     germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true)
     germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true)
     panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz'], checkIfExists: true)
     panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz_tbi'], checkIfExists: true)
 
-    GATK4_MUTECT2 ( input , run_single , run_pon , run_mito , interval_label , fasta , fastaidx , dict , germline_resource, germline_resource_tbi , panel_of_normals , panel_of_normals_tbi )
+    GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, interval_label, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
 }
 
 workflow test_gatk4_mutect2_generate_pon {
@@ -80,14 +80,14 @@ workflow test_gatk4_mutect2_generate_pon {
     run_mito = false
     interval_label = []
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
     dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
     germline_resource = []
     germline_resource_tbi = []
     panel_of_normals = []
     panel_of_normals_tbi = []
 
-    GATK4_MUTECT2 ( input , run_single , run_pon, run_mito , interval_label , fasta , fastaidx , dict , germline_resource, germline_resource_tbi , panel_of_normals , panel_of_normals_tbi )
+    GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, interval_label, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
 }
 
 // mitochondria mode would ideally have some mitochondria test data, but since the mitochondria settings only increase detection sensitivity, we can use the chr22 data as a stand in as it is already a small dataset, the extra variants detected compared to generate_pon shows the mode is working.
@@ -102,12 +102,12 @@ workflow test_gatk4_mutect2_mitochondria {
     run_mito = true
     interval_label = 'chr22'
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
     dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
     germline_resource = []
     germline_resource_tbi = []
     panel_of_normals = []
     panel_of_normals_tbi = []
 
-    GATK4_MUTECT2 ( input , run_single , run_pon, run_mito , interval_label , fasta , fastaidx , dict , germline_resource, germline_resource_tbi , panel_of_normals , panel_of_normals_tbi )
+    GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, interval_label, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
 }

tests/subworkflows/nf-core/gatk_create_som_pon/main.nf

@@ -16,11 +16,10 @@ workflow test_gatk_create_som_pon {
                     [] ]
                     ]
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
     dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
     pon_name = "test_panel"
     interval_file = file(params.test_data['homo_sapiens']['genome']['genome_interval_list'], checkIfExists: true)
 
-    GATK_CREATE_SOM_PON ( ch_mutect2_in, fasta, fastaidx, dict, pon_name, interval_file )
+    GATK_CREATE_SOM_PON ( ch_mutect2_in, fasta, fai, dict, pon_name, interval_file )
-
 }