Add metro map and update documentation to pass lint

ghga-de · Aug 23, 2023 · b1f6e20 · b1f6e20
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Showing 17 changed files with 768 additions and 99 deletions.
diff --git a/.ipynb_checkpoints/README-checkpoint.md b/.ipynb_checkpoints/README-checkpoint.md
@@ -14,9 +14,7 @@
 
 **buildrnaseqbundle** is a bioinformatics pipeline that can be used to create bundles of input data (genome files, annotations, indexes etc) for RNA sequencing analyses with **nf-core/rnaseq**, using the [guidelines for GTEx v10](https://github.com/broadinstitute/gtex-pipeline/blob/master/TOPMed_RNAseq_pipeline.md). 
 
-<!-- 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 -->
+[](buildrnaseqbundle-metro-map.drawio.png)
 
 1. Get the input fasta and gtf files 
     1. Prepre the reference genome file
@@ -41,17 +39,10 @@
 
 You can run the pipeline using:
 
-<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
-
 ```bash
 nextflow run nf-core/buildrnaseqbundle \
    -profile <docker/singularity/.../institute> \
-   --gencodeVersion           "44" \
    --spliceJunctionOverhang    100 \
-   --star_output_zip           <STAR_OUTPUT_ZIP> \
-   --rsem_output_zip           <RSEM_OUTPUT_ZIP> \
-   --executor                  <slurm/local>
-   --publish_intermediate_data <true/false>
    --outdir                    <OUTDIR>
 ```
 

diff --git a/.ipynb_checkpoints/modules-checkpoint.json b/.ipynb_checkpoints/modules-checkpoint.json
@@ -0,0 +1,67 @@
+{
+    "name": "nf-core/buildrnaseqbundle",
+    "homePage": "https://github.com/nf-core/buildrnaseqbundle",
+    "repos": {
+        "https://github.com/nf-core/modules.git": {
+            "modules": {
+                "nf-core": {
+                    "cat/cat": {
+                        "branch": "master",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "installed_by": ["modules"]
+                    },
+                    "cat/fastq": {
+                        "branch": "master",
+                        "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
+                        "installed_by": ["modules"]
+                    },
+                    "custom/dumpsoftwareversions": {
+                        "branch": "master",
+                        "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
+                        "installed_by": ["modules"]
+                    },
+                    "gatk4/createsequencedictionary": {
+                        "branch": "master",
+                        "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0",
+                        "installed_by": ["modules"]
+                    },
+                    "gunzip": {
+                        "branch": "master",
+                        "git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57",
+                        "installed_by": ["modules"]
+                    },
+                    "picard/createsequencedictionary": {
+                        "branch": "master",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "installed_by": ["modules"]
+                    },
+                    "rsem/preparereference": {
+                        "branch": "master",
+                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
+                        "installed_by": ["modules"]
+                    },
+                    "samtools/faidx": {
+                        "branch": "master",
+                        "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe",
+                        "installed_by": ["modules"]
+                    },
+                    "star/genomegenerate": {
+                        "branch": "master",
+                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
+                        "installed_by": ["modules"]
+                    },
+                    "untar": {
+                        "branch": "master",
+                        "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8",
+                        "installed_by": ["modules"]
+                    },
+                    "unzip": {
+                        "branch": "master",
+                        "git_sha": "cf67a6d7d043e2bd6a3099be84c72046fc71508f",
+                        "installed_by": ["modules"]
+                    }
+                }
+            }
+        }
+    }
+}
diff --git a/.ipynb_checkpoints/nextflow-checkpoint.config b/.ipynb_checkpoints/nextflow-checkpoint.config
@@ -8,17 +8,17 @@
 
 // Global default params, used in configs
 params {
-    gencodeVersion              = "44"
+    gencodeVersion              = 44
     spliceJunctionOverhang      = 100 // Length of reads - 1
     star_output_zip             = "STARv2710a_genome_GRCh38_noALT_noHLA_noDecoy_ERCC_v44_oh100"
     rsem_output_zip             = "rsem_reference_GRCh38_gencode44_ercc"
     executor                    = "slurm"
-    publish_intermediate_data   = null
+    publish_intermediate_data   = false
 
     // Boilerplate options
-    input                      = null
     outdir                     = "rnaseq-hg38-gencode.v44-bundle"
     publish_dir_mode           = 'copy'
+    input                      = null
     email                      = null
     email_on_fail              = null
     plaintext_email            = false

diff --git a/README.md b/README.md
@@ -14,9 +14,7 @@
 
 **buildrnaseqbundle** is a bioinformatics pipeline that can be used to create bundles of input data (genome files, annotations, indexes etc) for RNA sequencing analyses with **nf-core/rnaseq**, using the [guidelines for GTEx v10](https://github.com/broadinstitute/gtex-pipeline/blob/master/TOPMed_RNAseq_pipeline.md). 
 
-<!-- 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 -->
+[](buildrnaseqbundle-metro-map.drawio.png)
 
 1. Get the input fasta and gtf files 
     1. Prepre the reference genome file
@@ -41,17 +39,10 @@
 
 You can run the pipeline using:
 
-<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
-
 ```bash
 nextflow run nf-core/buildrnaseqbundle \
    -profile <docker/singularity/.../institute> \
-   --gencodeVersion           "44" \
    --spliceJunctionOverhang    100 \
-   --star_output_zip           <STAR_OUTPUT_ZIP> \
-   --rsem_output_zip           <RSEM_OUTPUT_ZIP> \
-   --executor                  <slurm/local>
-   --publish_intermediate_data <true/false>
    --outdir                    <OUTDIR>
 ```