Merge pull request #17 from a4000/dev

updated nf-core modules, made more parameters visible to user, and added workflow diagram
nf-core · Nov 27, 2023 · a147376 · a147376
2 parents f538a00 + de73299
commit a147376
Show file tree

Hide file tree

Showing 57 changed files with 518 additions and 117 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.0 - [date]
+## 1.0.0 - [date]
 
 Initial release of nf-core/readsimulator, created with the [nf-core](https://nf-co.re/) template.
 

diff --git a/README.md b/README.md
@@ -14,9 +14,9 @@
 
 **nf-core/readsimulator** is a pipeline to simulate sequencing reads. The pipeline currently supports simulating Amplicon, Target Capture, Metagenome, and Wholegenome data. It takes a samplesheet with sample names and seeds for random generation to produce simulated fastq files and a samplesheet that contains the paths to the fastq files.
 
-<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
-     workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
-<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
+<p align="center">
+    <img src="docs/images/readsimulator_workflow.png" alt="nf-core/readsimulator workflow overview" width="60%">
+</p>
 
 ### Amplicon simulation steps
 

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/readsimulator/releases/tag/1.0" target="_blank">nf-core/readsimulator</a>
+  This report has been generated by the <a href="https://github.com/nf-core/readsimulator/releases/tag/1.0.0" target="_blank">nf-core/readsimulator</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/readsimulator/1.0/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/readsimulator/1.0.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-readsimulator-methods-description":
     order: -1000

diff --git a/conf/modules.config b/conf/modules.config
@@ -42,18 +42,22 @@ process {
         ]
     }
 
-    withName: CAPSIM_ILLUMINA {
-        ext.args = "--fmedian 500 --num 500000 --illen 150 --miseq"
-        publishDir = [
-            path: { "${params.outdir}/capsim_illumina" },
-            mode: params.publish_dir_mode
-        ]
-    }
-
-    withName: CAPSIM_PACBIO {
-        ext.args = "--fmedian 500 --num 500000 --pacbio"
+    withName: JAPSA_CAPSIM {
+        ext.args = [
+            "--fmedian ${params.target_capture_fmedian}",
+            "--fshape ${params.target_capture_fshape}",
+            "--smedian ${params.target_capture_smedian}",
+            "--sshape ${params.target_capture_sshape}",
+            params.target_capture_tmedian ? "--tmedian ${params.target_capture_tmedian}" : "",
+            params.target_capture_tshape ? "--tshape ${params.target_capture_tshape}" : "",
+            "--num ${params.target_capture_num}",
+            params.target_capture_mode == "illumina" ?
+                "--illen ${params.target_capture_illen}" : "--pblen ${params.target_capture_pblen}",
+            params.target_capture_mode == "illumina" ?
+                "--ilmode ${params.target_capture_ilmode} --miseq" : "--pacbio"
+        ].join(' ').trim()
         publishDir = [
-            path: { "${params.outdir}/capsim_pacbio" },
+            path: { "${params.outdir}/capsim" },
             mode: params.publish_dir_mode
         ]
     }

diff --git a/docs/images/readsimulator_workflow.png b/docs/images/readsimulator_workflow.png
diff --git a/docs/images/readsimulator_workflow.svg b/docs/images/readsimulator_workflow.svg
diff --git a/modules.json b/modules.json
@@ -13,32 +13,32 @@
                     },
                     "bowtie2/align": {
                         "branch": "master",
-                        "git_sha": "fe54581f8bed20e4c4a51c616c93fd3379d89820",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "bowtie2/build": {
                         "branch": "master",
-                        "git_sha": "6a24fbe314bb2e6fe6306c29a63076ea87e8eb3c",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543",
+                        "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "f2d63bd5b68925f98f572eed70993d205cc694b7",
+                        "git_sha": "214d575774c172062924ad3564b4f66655600730",
                         "installed_by": ["modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "5394565c5fe4c760e5b35977ec7607c62e81d1f8",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/modules/local/crabs/dbdownload/environment.yml b/modules/local/crabs/dbdownload/environment.yml
@@ -0,0 +1,7 @@
+name: crabs_dbdownload
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::crabs=0.1.1-0
diff --git a/modules/local/crabs_dbdownload.nf → modules/local/crabs/dbdownload/main.nf b/modules/local/crabs_dbdownload.nf → modules/local/crabs/dbdownload/main.nf
@@ -4,7 +4,7 @@ process CRABS_DBDOWNLOAD {
     label 'process_medium'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
-    conda "bioconda::crabs=0.1.1-0"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/crabs:0.1.1--pyhb7b1952_0':
         'biocontainers/crabs:0.1.1--pyhb7b1952_0' }"

diff --git a/modules/local/crabs/dbimport/environment.yml b/modules/local/crabs/dbimport/environment.yml
@@ -0,0 +1,7 @@
+name: crabs_dbimport
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::crabs=0.1.1-0
diff --git a/modules/local/crabs_dbimport.nf → modules/local/crabs/dbimport/main.nf b/modules/local/crabs_dbimport.nf → modules/local/crabs/dbimport/main.nf
@@ -3,7 +3,7 @@ process CRABS_DBIMPORT {
     label 'process_medium'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
-    conda "bioconda::crabs=0.1.1-0"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/crabs:0.1.1--pyhb7b1952_0':
         'biocontainers/crabs:0.1.1--pyhb7b1952_0' }"

diff --git a/modules/local/crabs/insilicopcr/environment.yml b/modules/local/crabs/insilicopcr/environment.yml
@@ -0,0 +1,7 @@
+name: crabs_insilicopcr
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::crabs=0.1.1-0
diff --git a/modules/local/crabs_insilicopcr.nf → modules/local/crabs/insilicopcr/main.nf b/modules/local/crabs_insilicopcr.nf → modules/local/crabs/insilicopcr/main.nf
@@ -3,7 +3,7 @@ process CRABS_INSILICOPCR {
     label 'process_medium'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
-    conda "bioconda::crabs=0.1.1-0"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/crabs:0.1.1--pyhb7b1952_0':
         'biocontainers/crabs:0.1.1--pyhb7b1952_0' }"

diff --git a/modules/local/create_samplesheet.nf → ...s/local/custom/create_samplesheet/main.nf b/modules/local/create_samplesheet.nf → ...s/local/custom/create_samplesheet/main.nf
diff --git a/modules/local/custom/merge_samplesheets/environment.yml b/modules/local/custom/merge_samplesheets/environment.yml
@@ -0,0 +1,7 @@
+name: merge_samplesheet
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::sed=4.7
diff --git a/modules/local/merge_samplesheets.nf → ...s/local/custom/merge_samplesheets/main.nf b/modules/local/merge_samplesheets.nf → ...s/local/custom/merge_samplesheets/main.nf
@@ -2,7 +2,7 @@ process MERGE_SAMPLESHEETS {
     tag "$meta.id"
     label 'process_single'
 
-    conda "conda-forge::sed=4.7"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
         'nf-core/ubuntu:20.04' }"

diff --git a/modules/local/insilicoseq/generate/environment.yml b/modules/local/insilicoseq/generate/environment.yml
@@ -0,0 +1,7 @@
+name: insilicoseq_generate
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::insilicoseq=1.6.0
diff --git a/modules/local/insilicoseq_generate.nf → modules/local/insilicoseq/generate/main.nf b/modules/local/insilicoseq_generate.nf → modules/local/insilicoseq/generate/main.nf
@@ -2,14 +2,13 @@ process INSILICOSEQ_GENERATE {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::insilicoseq=1.6.0"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/insilicoseq:1.6.0--pyh7cba7a3_0':
         'biocontainers/insilicoseq:1.6.0--pyh7cba7a3_0' }"
 
     input:
-    path(fasta)
-    val(meta)
+    tuple val(meta), path(fasta)
 
     output:
     tuple val(meta), path("*.fastq.gz*"), emit: fastq

diff --git a/modules/local/japsa_capsim.nf → modules/local/japsa/capsim/main.nf b/modules/local/japsa_capsim.nf → modules/local/japsa/capsim/main.nf
diff --git a/modules/local/unzip/environment.yml b/modules/local/unzip/environment.yml
@@ -0,0 +1,7 @@
+name: unzip
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::unzip=6.0
diff --git a/modules/local/unzip.nf → modules/local/unzip/main.nf b/modules/local/unzip.nf → modules/local/unzip/main.nf
@@ -2,17 +2,15 @@ process UNZIP {
     tag "$file"
     label 'process_single'
 
-    conda "conda-forge::unzip=6.0"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/unzip:6.0':
         'biocontainers/unzip:6.0' }"
 
     input:
     path(file)
-    //tuple val(meta), path(file)
 
     output:
-    //tuple val(meta), path "unziped/*", emit: file
     path "unziped/*"   , emit: file
     path "versions.yml", emit: versions
 

diff --git a/modules/local/wgsim/environment.yml b/modules/local/wgsim/environment.yml
@@ -0,0 +1,7 @@
+name: wgsim
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::wgsim=1.0
diff --git a/modules/local/wgsim.nf → modules/local/wgsim/main.nf b/modules/local/wgsim.nf → modules/local/wgsim/main.nf
@@ -3,14 +3,13 @@ process WGSIM {
     label 'process_single'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
-    conda "bioconda::wgsim=1.0"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/wgsim:1.0--he4a0461_7':
         'biocontainers/wgsim:1.0--he4a0461_7' }"
 
     input:
-    path(fasta)
-    val(meta)
+    tuple val(meta), path(fasta)
 
     output:
     tuple val(meta), path("*.fq.gz*"), emit: fastq

diff --git a/modules/nf-core/bowtie2/align/environment.yml b/modules/nf-core/bowtie2/align/environment.yml
diff --git a/modules/nf-core/bowtie2/align/main.nf b/modules/nf-core/bowtie2/align/main.nf
diff --git a/modules/nf-core/bowtie2/align/meta.yml b/modules/nf-core/bowtie2/align/meta.yml
diff --git a/modules/nf-core/bowtie2/build/environment.yml b/modules/nf-core/bowtie2/build/environment.yml
diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf
diff --git a/modules/nf-core/bowtie2/build/meta.yml b/modules/nf-core/bowtie2/build/meta.yml
diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py