Alter location of the TSV's and add information to the output.md

.github/CONTRIBUTING.md

@@ -9,9 +9,7 @@ Please use the pre-filled template to save time.
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
-:::info
-If you need help using or modifying nf-core/mhcquant then the best place to ask is on the nf-core Slack [#mhcquant](https://nfcore.slack.com/channels/mhcquant) channel ([join our Slack here](https://nf-co.re/join/slack)).
-:::
+> If you need help using or modifying nf-core/mhcquant then the best place to ask is on the nf-core Slack [#mhcquant](https://nfcore.slack.com/channels/mhcquant) channel ([join our Slack here](https://nf-co.re/join/slack)).
 
 ## Contribution workflow
 
@@ -118,3 +116,4 @@ To get started:
 Devcontainer specs:
 
 - [DevContainer config](.devcontainer/devcontainer.json)
+- [Dockerfile](.devcontainer/Dockerfile)

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -42,9 +42,9 @@ body:
     attributes:
       label: System information
       description: |
-        * Nextflow version _(eg. 23.04.0)_
+        * Nextflow version _(eg. 22.10.1)_
         * 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 or Charliecloud)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
         * Version of nf-core/mhcquant _(eg. 1.1, 1.5, 1.8.2)_

.github/PULL_REQUEST_TEMPLATE.md

@@ -15,8 +15,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/mhcq
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/mhcquant/tree/master/.github/CONTRIBUTING.md)
-- [ ] If necessary, also make a PR on the nf-core/mhcquant _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/mhcquant/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/mhcquant _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.

.github/workflows/branch.yml

@@ -13,7 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == 'nf-core/mhcquant'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/mhcquant ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/mhcquant ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # If the above check failed, post a comment on the PR explaining the failure
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets

.github/workflows/linting.yml

@@ -78,7 +78,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.11"
+          python-version: "3.7"
           architecture: "x64"
 
       - name: Install dependencies

conf/modules.config

@@ -238,7 +238,7 @@ process {
 
     withName: 'OPENMS_TEXTEXPORTER' {
         publishDir  = [
-            path: {"${params.outdir}/intermediate_results/text_exporter"},
+            path: {"${params.outdir}/"},
             mode: params.publish_dir_mode,
             pattern: '*.tsv'
         ]
@@ -255,7 +255,7 @@ process {
 
     withName: 'REWRITE_QUANT_TSV' {
         publishDir  = [
-            path: {"${params.outdir}"},
+            path: {"${params.outdir}/modified_tsv"},
             mode: params.publish_dir_mode,
             pattern: '*.tsv'
         ]

docs/output.md

@@ -12,6 +12,7 @@ The directories listed below will be created in the results directory after the
 
 - `*.mzTab`
 - `*.tsv`
+- `/modified_tsv/*.tsv`
 
 The mzTab output file follows the a [HUPO-PSI format](<https://www.mcponline.org/article/S1535-9476(20)32821-8/fulltext>) and combines all information of the sample-condition group extracted from a database search throughout the pipeline. A detailed explanation of the respective entries are elaborately explained [here](https://psidev.info/sites/default/files/2017-07/R2_The_ten_minute_guide_to_mzTab.pdf). MzTab files are compatible with the PRIDE Archive - proteomics data repository and can be uploaded as search files.
 
@@ -61,6 +62,8 @@ PEPTIDE contains information about peptide hits that were identified and corresp
 #PEPTIDE        rt      mz      score   rank    sequence        charge  aa_before       aa_after        score_type      search_identifier       accessions      FFId_category   fea
 ```
 
+Lastly, the TSV output that comprising similar information to the mzTab output, mentioned above is also available in an alternative TSV format (found in `modified_tsv/`). In this document peptide and consensus information is available in line. Furthermore, information regarding the modification and sequence are expanded, including the sequence without modifications and adding the information of the modification in an additional column.
+
 ### Intermediate results
 
 <details  markdown="1">

lib/NfcoreTemplate.groovy

@@ -3,7 +3,6 @@
 //
 
 import org.yaml.snakeyaml.Yaml
-import groovy.json.JsonOutput
 
 class NfcoreTemplate {
 
@@ -129,7 +128,7 @@ class NfcoreTemplate {
         def email_html    = html_template.toString()
 
         // Render the sendmail template
-        def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit
+        def max_multiqc_email_size = params.max_multiqc_email_size as nextflow.util.MemoryUnit
         def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ]
         def sf                     = new File("$projectDir/assets/sendmail_template.txt")
         def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
@@ -223,21 +222,6 @@ class NfcoreTemplate {
         }
     }
 
-    //
-    // Dump pipeline parameters in a json file
-    //
-    public static void dump_parameters(workflow, params) {
-        def output_d = new File("${params.outdir}/pipeline_info/")
-        if (!output_d.exists()) {
-            output_d.mkdirs()
-        }
-
-        def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
-        def output_pf  = new File(output_d, "params_${timestamp}.json")
-        def jsonStr    = JsonOutput.toJson(params)
-        output_pf.text = JsonOutput.prettyPrint(jsonStr)
-    }
-
     //
     // Print pipeline summary on completion
     //