Merge branch 'TEMPLATE' into rename_pipeline

JaneliaSciComp · Oct 6, 2023 · 3e29e21 · 3e29e21
2 parents cdc2ae3 + 429784b
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -9,42 +9,53 @@ body:
 
         - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
         - [JaneliaSciComp/easifish pipeline documentation](https://nf-co.re/easifish/usage)
-
   - type: textarea
     id: description
     attributes:
       label: Description of the bug
       description: A clear and concise description of what the bug is.
     validations:
       required: true
-
   - type: textarea
     id: command_used
     attributes:
       label: Command used and terminal output
-      description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
+      description: Steps to reproduce the behaviour. Please paste the command you used
+        to launch the pipeline and the output from your terminal.
       render: console
-      placeholder: |
-        $ nextflow run ...
+      placeholder: "$ nextflow run ...
+
 
         Some output where something broke
 
+        "
   - type: textarea
     id: files
     attributes:
       label: Relevant files
-      description: |
-        Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed.
-        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.
+      description: "Please drag and drop the relevant files here. Create a `.zip` archive
+        if the extension is not allowed.
 
+        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file
+        in the directory where you launched the pipeline)_ as well as custom Nextflow
+        configuration files.
+
+        "
   - type: textarea
     id: system
     attributes:
       label: System information
-      description: |
-        * Nextflow version _(eg. 23.04.0)_
+      description: "* Nextflow version _(eg. 23.04.0)_
+
         * Hardware _(eg. HPC, Desktop, Cloud)_
+
         * Executor _(eg. slurm, local, awsbatch)_
-        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
+
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud,
+        or Apptainer)_
+
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
+
         * Version of JaneliaSciComp/easifish _(eg. 1.1, 1.5, 1.8.2)_
+
+        "
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,6 +1,29 @@
+lint:
+  files_exist:
+    - CODE_OF_CONDUCT.md
+    - assets/nf-core-janeliascicomp-easifish_logo_light.png
+    - docs/images/nf-core-janeliascicomp-easifish_logo_light.png
+    - docs/images/nf-core-janeliascicomp-easifish_logo_dark.png
+    - .github/ISSUE_TEMPLATE/config.yml
+    - .github/workflows/awstest.yml
+    - .github/workflows/awsfulltest.yml
+    - conf/igenomes.config
+  files_unchanged:
+    - CODE_OF_CONDUCT.md
+    - assets/nf-core-janeliascicomp-easifish_logo_light.png
+    - docs/images/nf-core-janeliascicomp-easifish_logo_light.png
+    - docs/images/nf-core-janeliascicomp-easifish_logo_dark.png
+    - .github/ISSUE_TEMPLATE/bug_report.yml
+  multiqc_config:
+    - report_comment
+  nextflow_config:
+    - manifest.name
+    - manifest.homePage
+  readme:
+    - nextflow_badge
 repository_type: pipeline
 template:
   prefix: JaneliaSciComp
   skip:
-  - github_badges
-  - igenomes
+    - github_badges
+    - igenomes
diff --git a/CITATIONS.md b/CITATIONS.md
@@ -20,6 +20,8 @@
 
   > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
+  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
+
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
   > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

diff --git a/README.md b/README.md
@@ -87,7 +87,7 @@ If you use `JaneliaSciComp/easifish` for your analysis, please cite the EASI-FIS
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
-You can cite the `nf-core` publication as follows:
+This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).
 
 > **The nf-core framework for community-curated bioinformatics pipelines.**
 >

diff --git a/assets/nf-core-lightsheetrecon_logo_light.png b/assets/nf-core-lightsheetrecon_logo_light.png
diff --git a/docs/README.md b/docs/README.md
@@ -6,5 +6,3 @@ The JaneliaSciComp/easifish documentation is split into the following pages:
   - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags.
 - [Output](output.md)
   - An overview of the different results produced by the pipeline and how to interpret them.
-
-You can find a lot more documentation about installing, configuring and running nf-core pipelines on the website: [https://nf-co.re](https://nf-co.re)
diff --git a/docs/images/nf-core-lightsheetrecon_logo_dark.png b/docs/images/nf-core-lightsheetrecon_logo_dark.png
diff --git a/docs/images/nf-core-lightsheetrecon_logo_light.png b/docs/images/nf-core-lightsheetrecon_logo_light.png
diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
@@ -339,11 +339,6 @@ class NfcoreTemplate {
         String.format(
             """\n
             ${dashedLine(monochrome_logs)}
-                                                    ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
-            ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
-            ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
-            ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
-                                                    ${colors.green}`._,._,\'${colors.reset}
             ${colors.purple}  ${workflow.manifest.name} ${workflow_version}${colors.reset}
             ${dashedLine(monochrome_logs)}
             """.stripIndent()

diff --git a/lib/WorkflowEASIFISH.groovy b/lib/WorkflowEASIFISH.groovy
@@ -1,17 +1,32 @@
 //
+<<<<<<<< HEAD:lib/WorkflowEASIFISH.groovy
 // This file holds several functions specific to the workflow/easifish.nf in the JaneliaSciComp/easifish pipeline
+========
+// This file holds several functions specific to the workflow/janeliascicomp-easifish.nf in the JaneliaSciComp/easifish pipeline
+>>>>>>>> TEMPLATE:lib/WorkflowJaneliascicomp-easifish.groovy
 //
 
 import nextflow.Nextflow
 import groovy.text.SimpleTemplateEngine
 
+<<<<<<<< HEAD:lib/WorkflowEASIFISH.groovy
 class WorkflowEASIFISH {
+========
+class WorkflowJaneliascicomp-easifish {
+>>>>>>>> TEMPLATE:lib/WorkflowJaneliascicomp-easifish.groovy
 
     //
     // Check and validate parameters
     //
     public static void initialise(params, log) {
 
+<<<<<<<< HEAD:lib/WorkflowEASIFISH.groovy
+========
+
+        if (!params.fasta) {
+            Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
+        }
+>>>>>>>> TEMPLATE:lib/WorkflowJaneliascicomp-easifish.groovy
     }
 
     //
@@ -46,9 +61,19 @@ class WorkflowEASIFISH {
     //
 
     public static String toolCitationText(params) {
+<<<<<<<< HEAD:lib/WorkflowEASIFISH.groovy
         def citation_text = [
                 "Tools used in the workflow included:",
                 "stitching-spark (https://github.com/saalfeldlab/stitching-spark),",
+========
+
+        // TODO nf-core: Optionally add in-text citation tools to this list.
+        // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "",
+        // Uncomment function in methodsDescriptionText to render in MultiQC report
+        def citation_text = [
+                "Tools used in the workflow included:",
+                "FastQC (Andrews 2010),",
+>>>>>>>> TEMPLATE:lib/WorkflowJaneliascicomp-easifish.groovy
                 "MultiQC (Ewels et al. 2016)",
                 "."
             ].join(' ').trim()
@@ -57,7 +82,16 @@ class WorkflowEASIFISH {
     }
 
     public static String toolBibliographyText(params) {
+<<<<<<<< HEAD:lib/WorkflowEASIFISH.groovy
         def reference_text = [
+========
+
+        // TODO Optionally add bibliographic entries to this list.
+        // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "<li>Author (2023) Pub name, Journal, DOI</li>" : "",
+        // Uncomment function in methodsDescriptionText to render in MultiQC report
+        def reference_text = [
+                "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</li>",
+>>>>>>>> TEMPLATE:lib/WorkflowJaneliascicomp-easifish.groovy
                 "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"
             ].join(' ').trim()
 
@@ -75,15 +109,26 @@ class WorkflowEASIFISH {
         meta["nodoi_text"] = meta.manifest_map.doi ? "": "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
 
         // Tool references
+<<<<<<<< HEAD:lib/WorkflowEASIFISH.groovy
         meta["tool_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
         meta["tool_bibliography"] = toolBibliographyText(params)
+========
+        meta["tool_citations"] = ""
+        meta["tool_bibliography"] = ""
+
+        // TODO Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
+        //meta["tool_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
+        //meta["tool_bibliography"] = toolBibliographyText(params)
+
+>>>>>>>> TEMPLATE:lib/WorkflowJaneliascicomp-easifish.groovy
 
         def methods_text = mqc_methods_yaml.text
 
         def engine =  new SimpleTemplateEngine()
         def description_html = engine.createTemplate(methods_text).make(meta)
 
         return description_html
+<<<<<<<< HEAD:lib/WorkflowEASIFISH.groovy
     }
 
     //
@@ -100,3 +145,6 @@ class WorkflowEASIFISH {
         }
     }
 }
+========
+    }}
+>>>>>>>> TEMPLATE:lib/WorkflowJaneliascicomp-easifish.groovy
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
@@ -53,15 +53,4 @@ class WorkflowMain {
             Nextflow.error("Please provide an outdir to the pipeline e.g. '--outdir ./output'")
         }
     }
-    //
-    // Get attribute from genome config file e.g. fasta
-    //
-    public static Object getGenomeAttribute(params, attribute) {
-        if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
-            if (params.genomes[ params.genome ].containsKey(attribute)) {
-                return params.genomes[ params.genome ][ attribute ]
-            }
-        }
-        return null
-    }
 }
diff --git a/main.nf b/main.nf
@@ -4,8 +4,6 @@
     JaneliaSciComp/easifish
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     Github : https://github.com/JaneliaSciComp/easifish
-    Website: https://nf-co.re/easifish
-    Slack  : https://nfcore.slack.com/channels/easifish
 ----------------------------------------------------------------------------------------
 */
 

diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -19,7 +19,7 @@
                     "mimetype": "text/csv",
                     "pattern": "^\\S+\\.csv$",
                     "description": "Path to comma-separated file containing information about the samples in the experiment.",
-                    "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/easifish/usage#samplesheet-input).",
+                    "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.",
                     "fa_icon": "fas fa-file-csv"
                 },
                 "indir": {