From b59e8054e4c7b92407179d7e280b015dbfaf28a6 Mon Sep 17 00:00:00 2001
From: Kevin Menden <kevin.menden@t-online.de>
Date: Fri, 2 Jul 2021 13:31:09 +0200
Subject: [PATCH] fix rseqc/junctionsaturation (#553)

* bump bcftools filter

* junctionsaturation meta.yml and test

* pytest config entry

* bump bcftools version down again

* fix test

* fix bcftools
---
 software/rseqc/junctionsaturation/meta.yml    | 44 +++++++++++++++++++
 tests/config/pytest_software.yml              |  4 ++
 .../software/rseqc/junctionsaturation/main.nf | 16 +++++++
 .../rseqc/junctionsaturation/test.yml         |  9 ++++
 4 files changed, 73 insertions(+)
 create mode 100644 software/rseqc/junctionsaturation/meta.yml
 create mode 100644 tests/software/rseqc/junctionsaturation/main.nf
 create mode 100644 tests/software/rseqc/junctionsaturation/test.yml

diff --git a/software/rseqc/junctionsaturation/meta.yml b/software/rseqc/junctionsaturation/meta.yml
new file mode 100644
index 00000000..38008577
--- /dev/null
+++ b/software/rseqc/junctionsaturation/meta.yml
@@ -0,0 +1,44 @@
+name: rseqc_junctionsaturation
+description: compare detected splice junctions to reference gene model
+keywords:
+  - junctions
+  - splicing
+  - rnaseq
+tools:
+  - rseqc:
+      description: |
+        RSeQC package provides a number of useful modules that can comprehensively evaluate
+        high throughput sequence data especially RNA-seq data.
+      homepage: http://rseqc.sourceforge.net/
+      documentation: http://rseqc.sourceforge.net/
+      doi: 10.1093/bioinformatics/bts356
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: the alignment in bam format
+      pattern: "*.{bam}"
+  - bed:
+      type: file
+      description: a bed file for the reference gene model
+      pattern: "*.{bed}"
+output:
+  - pdf:
+      type: file
+      description: Junction saturation report
+      pattern: "*.pdf"
+  - rscript:
+      type: file
+      description: Junction saturation R-script
+      pattern: "*.r"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+authors:
+  - "@drpatelh"
+  - "@kevinmenden"
diff --git a/tests/config/pytest_software.yml b/tests/config/pytest_software.yml
index 6a32058f..c514b1fa 100644
--- a/tests/config/pytest_software.yml
+++ b/tests/config/pytest_software.yml
@@ -603,6 +603,10 @@ rseqc/junctionannotation:
   - software/rseqc/junctionannotation/**
   - tests/software/rseqc/junctionannotation/**
 
+rseqc/junctionsaturation:
+  - software/rseqc/junctionsaturation/**
+  - tests/software/rseqc/junctionsaturation/**
+
 rseqc/readdistribution:
   - software/rseqc/readdistribution/**
   - tests/software/rseqc/readdistribution/**
diff --git a/tests/software/rseqc/junctionsaturation/main.nf b/tests/software/rseqc/junctionsaturation/main.nf
new file mode 100644
index 00000000..15532a1f
--- /dev/null
+++ b/tests/software/rseqc/junctionsaturation/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RSEQC_JUNCTIONSATURATION }   from '../../../../software/rseqc/junctionsaturation/main.nf' addParams(options: [:])
+
+workflow test_rseqc_junctionsaturation {
+    input = [
+        [ 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_bed'], checkIfExists: true)
+
+    RSEQC_JUNCTIONSATURATION ( input, bed )
+}
diff --git a/tests/software/rseqc/junctionsaturation/test.yml b/tests/software/rseqc/junctionsaturation/test.yml
new file mode 100644
index 00000000..1ed6d719
--- /dev/null
+++ b/tests/software/rseqc/junctionsaturation/test.yml
@@ -0,0 +1,9 @@
+- name: rseqc junctionsaturation test_rseqc_junctionsaturation
+  command: nextflow run tests/software/rseqc/junctionsaturation -entry test_rseqc_junctionsaturation -c tests/config/nextflow.config
+  tags:
+    - rseqc/junctionsaturation
+    - rseqc
+  files:
+    - path: output/rseqc/test.junctionSaturation_plot.pdf
+    - path: output/rseqc/test.junctionSaturation_plot.r
+      md5sum: caa6e63dcb477aabb169882b2f30dadd