nf-core · alyssa-ab · Mar 13, 2023 · Mar 13, 2023 · Mar 15, 2023 · Mar 15, 2023
diff --git a/README.md b/README.md
@@ -2,6 +2,7 @@
 
 [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/viralintegration/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7783480-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7783480)
 
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)

diff --git a/docs/usage.md b/docs/usage.md
@@ -61,7 +61,7 @@ By default, the pipeline uses the [CTAT-VIF human virus database](https://github
 The typical command for running the pipeline is as follows:
 
 ```bash
-nextflow run nf-core/viralintegration --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker
+nextflow run nf-core/viralintegration --input ./samplesheet.csv --outdir ./results --genome GRCh38 -profile docker
 ```
 
 This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
@@ -92,7 +92,8 @@ with `params.yaml` containing:
 ```yaml
 input: './samplesheet.csv'
 outdir: './results/'
-genome: 'GRCh37'
+genome: 'GRCh38'
+input: 'data'
 <...>
 ```
 

diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
@@ -4,6 +4,8 @@
 
 import nextflow.Nextflow
 
+import nextflow.Nextflow
+
 class WorkflowMain {
 
     //

diff --git a/lib/WorkflowViralintegration.groovy b/lib/WorkflowViralintegration.groovy
@@ -12,6 +12,7 @@ class WorkflowViralintegration {
     //
     public static void initialise(params, log) {
 
+
         genomeExistsError(params, log)
 
 

diff --git a/modules.json b/modules.json
@@ -7,44 +7,44 @@
                 "nf-core": {
                     "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": "1537442a7be4a78efa3d1ff700a923c627bbda5d",
                         "installed_by": ["modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "5394565c5fe4c760e5b35977ec7607c62e81d1f8",
                         "installed_by": ["modules"]
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "star/align": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "9f6b233518f7d9ecdcf24b798b7e491db5424273",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/star/align/star-align.diff"
                     },
                     "star/genomegenerate": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "0e98289b5bec6e3f8f588a8a9d05e8aacc1179a0",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/star/genomegenerate/star-genomegenerate.diff"
                     },
                     "trimmomatic": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/trimmomatic/trimmomatic.diff"
                     }

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
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml
diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test
diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap
diff --git a/modules/nf-core/fastqc/tests/tags.yml b/modules/nf-core/fastqc/tests/tags.yml
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml