Finish rseqc modules (#439)

* initial 'modules create' of minia

* fixed tests

* finished meta.yml

* fixed filters.yml

* resolved issues in pytest_software.yml

* add newline

* Update software/minia/main.nf

* fixing a bunch of module tests

* remove vscode

* fixed minia

* added rseqc/bamstat tests

* added tests/meta.yml for rseqc/inferexperiment

* added test/meta.yml for rseqc/inner_distances

* added meta.yml and tests/main.nf for junctionannotation (test not running)

* added test/meta.yml for rseqc/readdistribution

* finished test/meta.yml for rseqc/readduplication

* added entries to pytest_software.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

software/rseqc/bamstat/meta.yml

@@ -0,0 +1,36 @@
+name: rseqc_bamstat
+description: Generate statistics from a bam file
+keywords:
+  - bam
+  - qc
+  - bamstat
+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 bam file to calculate statistics of
+      pattern: "*.{bam}"
+output:
+  - txt:
+      type: file
+      description: bam statistics report
+      pattern: "*.bam_stat.txt"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+authors:
+  - "@drpatelh"
+  - "@kevinmenden"

software/rseqc/inferexperiment/meta.yml

@@ -0,0 +1,39 @@
+name: rseqc_inferexperiment
+description: Infer strandedness from sequencing reads
+keywords:
+  - rnaseq
+  - experiment
+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 bam file to calculate statistics of
+      pattern: "*.{bam}"
+  - bed:
+      type: file
+      description: a bed file for the reference gene model
+      pattern: "*.{bed}"
+output:
+  - txt:
+      type: file
+      description: infer_experiment results report
+      pattern: "*.infer_experiment.txt"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+authors:
+  - "@drpatelh"
+  - "@kevinmenden"

software/rseqc/innerdistance/meta.yml

@@ -0,0 +1,55 @@
+name: rseqc_innerdistance
+description: Calculate inner distance between read pairs.
+keywords:
+  - fragment_size
+  - inner_distance
+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:
+  - distance:
+      type: file
+      description: the inner distances
+      pattern: "*.inner_distance.txt"
+  - freq:
+      type: file
+      description: frequencies of different insert sizes
+      pattern: "*.inner_distance_freq.txt"
+  - mean:
+      type: file
+      description: mean/median values of inner distances
+      pattern: "*.inner_distance_mean.txt"
+  - pdf:
+      type: file
+      description: distribution plot of inner distances
+      pattern: "*.inner_distance_plot.pdf"
+  - rscript:
+      type: file
+      description: script to reproduce the plot
+      pattern: "*.inner_distance_plot.R"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+authors:
+  - "@drpatelh"
+  - "@kevinmenden"

software/rseqc/junctionannotation/meta.yml

@@ -0,0 +1,61 @@
+name: rseqc_innerdistance
+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:
+  - bed:
+      type: file
+      description: bed file of annotated junctions
+      pattern: "*.junction.bed"
+  - interact_bed:
+      type: file
+      description: Interact bed file
+      pattern: "*.Interact.bed"
+  - xls:
+      type: file
+      description: xls file with junction information
+      pattern: "*.xls"
+  - pdf:
+      type: file
+      description: junction plot
+      pattern: "*.junction.pdf"
+  - events_pdf:
+      type: file
+      description: events plot
+      pattern: "*.events.pdf"
+  - rscript:
+      type: file
+      description: Rscript to reproduce the plots
+      pattern: "*.r"
+  - log:
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+authors:
+  - "@drpatelh"
+  - "@kevinmenden"

software/rseqc/readdistribution/meta.yml

@@ -0,0 +1,40 @@
+name: rseqc_readdistribution
+description: Calculate how mapped reads are distributed over genomic features
+keywords:
+  - read distribution
+  - genomics
+  - 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:
+  - txt:
+      type: file
+      description: the read distribution report
+      pattern: "*.read_distribution.txt"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+authors:
+  - "@drpatelh"
+  - "@kevinmenden"

software/rseqc/readduplication/meta.yml

@@ -0,0 +1,51 @@
+name: rseqc_readduplication
+description: Calculate read duplication rate
+keywords:
+  - rnaseq
+  - duplication
+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:
+  - seq_xls:
+      type: file
+      description: Read duplication rate determined from mapping position of read
+      pattern: "*seq.DupRate.xls"
+  - pos_xls:
+      type: file
+      description: Read duplication rate determined from sequence of read
+      pattern: "*pos.DupRate.xls"
+  - pdf:
+      type: file
+      description: plot of duplication rate
+      pattern: "*.pdf"
+  - rscript:
+      type: file
+      description: script to reproduce the plot
+      pattern: "*.R"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+authors:
+  - "@drpatelh"
+  - "@kevinmenden"

tests/config/pytest_software.yml

@@ -411,6 +411,26 @@ rasusa:
   - software/rasusa/**
   - tests/software/rasusa/**
 
+rseqc/bamstat:
+  - software/rseqc/bamstat/**
+  - tests/software/rseqc/bamstat/**
+
+rseqc/inferexperiment:
+  - software/rseqc/inferexperiment/**
+  - tests/software/rseqc/inferexperiment/**
+
+rseqc/innerdistance:
+  - software/rseqc/innerdistance/**
+  - tests/software/rseqc/innerdistance/**
+
+rseqc/readdistribution:
+  - software/rseqc/readdistribution/**
+  - tests/software/rseqc/readdistribution/**
+
+rseqc/readduplication:
+  - software/rseqc/readduplication/**
+  - tests/software/rseqc/readduplication/**
+
 salmon/index:
   - software/salmon/index/**
   - tests/software/salmon/index/**

tests/software/rseqc/bamstat/main.nf

@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RSEQC_BAMSTAT }   from '../../../../software/rseqc/bamstat/main.nf'   addParams(options: [:])
+
+workflow test_rseqc_bamstat {
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+            ]
+
+    RSEQC_BAMSTAT ( input )
+}

tests/software/rseqc/bamstat/test.yml

@@ -0,0 +1,8 @@
+- name: rseqc bamstat test_rseqc_bamstat
+  command: nextflow run tests/software/rseqc/bamstat -entry test_rseqc_bamstat -c tests/config/nextflow.config
+  tags:
+    - rseqc
+    - rseqc/bamstat
+  files:
+    - path: output/rseqc/test.bam_stat.txt
+      md5sum: 2675857864c1d1139b2a19d25dc36b09

tests/software/rseqc/inferexperiment/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RSEQC_INFEREXPERIMENT }   from '../../../../software/rseqc/inferexperiment/main.nf'   addParams(options: [:])
+
+workflow test_rseqc_inferexperiment {
+    input = [ [ id:'test' ], // 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_INFEREXPERIMENT ( input, bed )
+}

tests/software/rseqc/inferexperiment/test.yml

@@ -0,0 +1,8 @@
+- name: rseqc inferexperiment test_rseqc_inferexperiment
+  command: nextflow run tests/software/rseqc/inferexperiment -entry test_rseqc_inferexperiment -c tests/config/nextflow.config
+  tags:
+    - rseqc
+    - rseqc/inferexperiment
+  files:
+    - path: output/rseqc/test.infer_experiment.txt
+      md5sum: f9d0bfc239df637cd8aeda40ade3c59a

tests/software/rseqc/innerdistance/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RSEQC_INNERDISTANCE }   from '../../../../software/rseqc/innerdistance/main.nf'   addParams(options: [:])
+
+workflow test_rseqc_innerdistance {
+    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_bed12'], checkIfExists: true)
+
+    RSEQC_INNERDISTANCE ( input, bed )
+}

tests/software/rseqc/innerdistance/test.yml

@@ -0,0 +1,15 @@
+- name: rseqc innerdistance test_rseqc_innerdistance
+  command: nextflow run tests/software/rseqc/innerdistance -entry test_rseqc_innerdistance -c tests/config/nextflow.config
+  tags:
+    - rseqc
+    - rseqc/innerdistance
+  files:
+    - path: output/rseqc/test.inner_distance.txt
+      md5sum: a1acc9def0f64a5500d4c4cb47cbe32b
+    - path: output/rseqc/test.inner_distance_freq.txt
+      md5sum: 3fc037501f5899b5da009c8ce02fc25e
+    - path: output/rseqc/test.inner_distance_mean.txt
+      md5sum: 58398b7d5a29a5e564f9e3c50b55996c
+    - path: output/rseqc/test.inner_distance_plot.pdf
+    - path: output/rseqc/test.inner_distance_plot.r
+      md5sum: 5859fbd5b42046d47e8b9aa85077f4ea

tests/software/rseqc/junctionannotation/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RSEQC_JUNCTIONANNOTATION }   from '../../../../software/rseqc/junctionannotation/main.nf'   addParams(options: [:])
+
+workflow test_rseqc_junctionannotation {
+    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_bed12'], checkIfExists: true)
+
+    RSEQC_JUNCTIONANNOTATION ( input, bed )
+}

tests/software/rseqc/readdistribution/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RSEQC_READDISTRIBUTION }   from '../../../../software/rseqc/readdistribution/main.nf'   addParams(options: [:])
+
+workflow test_rseqc_readdistribution {
+    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_bed12'], checkIfExists: true)
+
+    RSEQC_READDISTRIBUTION ( input, bed )
+}

tests/software/rseqc/readdistribution/test.yml

@@ -0,0 +1,8 @@
+- name: rseqc readdistribution test_rseqc_readdistribution
+  command: nextflow run tests/software/rseqc/readdistribution -entry test_rseqc_readdistribution -c tests/config/nextflow.config
+  tags:
+    - rseqc
+    - rseqc/readdistribution
+  files:
+    - path: output/rseqc/test.read_distribution.txt
+      md5sum: 56893fdc0809d968629a363551a1655f

tests/software/rseqc/readduplication/main.nf

@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RSEQC_READDUPLICATION }   from '../../../../software/rseqc/readduplication/main.nf'   addParams(options: [:])
+
+workflow test_rseqc_readduplication {
+    input = [ [ id:'test', single_end: false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+            ]
+
+    RSEQC_READDUPLICATION ( input )
+}

tests/software/rseqc/readduplication/test.yml

@@ -0,0 +1,13 @@
+- name: rseqc readduplication test_rseqc_readduplication
+  command: nextflow run tests/software/rseqc/readduplication -entry test_rseqc_readduplication -c tests/config/nextflow.config
+  tags:
+    - rseqc/readduplication
+    - rseqc
+  files:
+    - path: output/rseqc/test.DupRate_plot.pdf
+    - path: output/rseqc/test.DupRate_plot.r
+      md5sum: 3c0325095cee4835b921e57d61c23dca
+    - path: output/rseqc/test.pos.DupRate.xls
+      md5sum: a859bc2031d46bf1cc4336205847caa3
+    - path: output/rseqc/test.seq.DupRate.xls
+      md5sum: ee8783399eec5a18522a6f08bece338b