Fix linting failures (#552)

* Modules TLC

* Fix all the tests

* Fix linting failures

* Soft-link build files to bypass lint error

* Update software/rseqc/junctionannotation/main.nf

software/rseqc/junctionannotation/main.nf

@@ -23,13 +23,13 @@ process RSEQC_JUNCTIONANNOTATION {
     path  bed
 
     output:
-    tuple val(meta), path("*.junction.bed"), emit: bed
-    tuple val(meta), path("*.Interact.bed"), emit: interact_bed
     tuple val(meta), path("*.xls")         , emit: xls
-    tuple val(meta), path("*junction.pdf") , emit: pdf
-    tuple val(meta), path("*events.pdf")   , emit: events_pdf
     tuple val(meta), path("*.r")           , emit: rscript
     tuple val(meta), path("*.log")         , emit: log
+    tuple val(meta), path("*.junction.bed"), optional:true, emit: bed
+    tuple val(meta), path("*.interact.bed"), optional:true, emit: interact_bed
+    tuple val(meta), path("*junction.pdf") , optional:true, emit: pdf
+    tuple val(meta), path("*events.pdf")   , optional:true, emit: events_pdf
     path  "*.version.txt"                  , emit: version
 
     script:

software/rseqc/junctionannotation/meta.yml

@@ -1,4 +1,4 @@
-name: rseqc_innerdistance
+name: rseqc_junctionannotation
 description: compare detected splice junctions to reference gene model
 keywords:
   - junctions

tests/config/pytest_software.yml

@@ -487,6 +487,10 @@ optitype:
   - software/optitype/**
   - tests/software/optitype/**
 
+pairix:
+  - software/pairix/**
+  - tests/software/pairix/**
+
 pairtools/dedup:
   - software/pairtools/dedup/**
   - tests/software/pairtools/dedup/**
@@ -499,6 +503,10 @@ pairtools/parse:
   - software/pairtools/parse/**
   - tests/software/pairtools/parse/**
 
+pairtools/restrict:
+  - software/pairtools/restrict/**
+  - tests/software/pairtools/restrict/**
+
 pairtools/select:
   - software/pairtools/select/**
   - tests/software/pairtools/select/**
@@ -583,6 +591,10 @@ rseqc/innerdistance:
   - software/rseqc/innerdistance/**
   - tests/software/rseqc/innerdistance/**
 
+rseqc/junctionannotation:
+  - software/rseqc/junctionannotation/**
+  - tests/software/rseqc/junctionannotation/**
+
 rseqc/readdistribution:
   - software/rseqc/readdistribution/**
   - tests/software/rseqc/readdistribution/**

tests/software/bowtie/build

@@ -0,0 +1 @@
+build_test/

tests/software/bowtie2/build

@@ -0,0 +1 @@
+build_test/

tests/software/hisat2/build

@@ -0,0 +1 @@
+build_test/

tests/software/rseqc/junctionannotation/main.nf

@@ -2,14 +2,15 @@
 
 nextflow.enable.dsl = 2
 
-include { RSEQC_JUNCTIONANNOTATION }   from '../../../../software/rseqc/junctionannotation/main.nf'   addParams(options: [:])
+include { RSEQC_JUNCTIONANNOTATION }   from '../../../../software/rseqc/junctionannotation/main.nf' addParams(options: [:])
 
 workflow test_rseqc_junctionannotation {
-    input = [ [ id:'test', single_end: false ], // meta map
+    input = [ 
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+        [ id:'test', single_end: false ], // meta map
-            ]
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+    ]
 
-    bed = file(params.test_data['sarscov2']['genome']['test_bed12'], checkIfExists: true)
+    bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
 
     RSEQC_JUNCTIONANNOTATION ( input, bed )
 }

tests/software/rseqc/junctionannotation/test.yml

@@ -0,0 +1,9 @@
+- name: rseqc junctionannotation test_rseqc_junctionannotation
+  command: nextflow run tests/software/rseqc/junctionannotation -entry test_rseqc_junctionannotation -c tests/config/nextflow.config
+  tags:
+    - rseqc
+    - rseqc/junctionannotation
+  files:
+    - path: output/rseqc/test.junction_annotation.log
+    - path: output/rseqc/test.junction.xls
+    - path: output/rseqc/test.junction_plot.r