Pipeline - draft1

.gitignore

@@ -7,3 +7,7 @@ testing/
 testing*
 *.pyc
 null/
+co2footprint*
+.nf-test/
+.nf-test.log
+.vscode

.nf-core.yml

@@ -1,67 +1,29 @@
 bump_version: null
 lint:
   files_exist:
-    - .github/ISSUE_TEMPLATE/bug_report.yml
-    - .github/ISSUE_TEMPLATE/feature_request.yml
-    - .github/PULL_REQUEST_TEMPLATE.md
-    - .github/CONTRIBUTING.md
-    - .github/.dockstore.yml
-    - conf/igenomes.config
+    - .github/ISSUE_TEMPLATE/config.yml
     - conf/igenomes_ignored.config
     - conf/igenomes.config
     - assets/email_template.html
     - assets/sendmail_template.txt
     - assets/email_template.txt
-    - .github/ISSUE_TEMPLATE/bug_report.yml
-    - .github/ISSUE_TEMPLATE/feature_request.yml
-    - .github/PULL_REQUEST_TEMPLATE.md
-    - .github/CONTRIBUTING.md
-    - .github/.dockstore.yml
-    - conf/igenomes.config
-    - conf/igenomes_ignored.config
-    - assets/email_template.html
-    - assets/sendmail_template.txt
-    - assets/email_template.txt
     - CODE_OF_CONDUCT.md
     - assets/nf-core-longreadmag_logo_light.png
     - docs/images/nf-core-longreadmag_logo_light.png
     - docs/images/nf-core-longreadmag_logo_dark.png
-    - .github/ISSUE_TEMPLATE/config.yml
     - .github/workflows/awstest.yml
     - .github/workflows/awsfulltest.yml
   files_unchanged:
-    - .github/ISSUE_TEMPLATE/bug_report.yml
-    - .github/ISSUE_TEMPLATE/config.yml
-    - .github/ISSUE_TEMPLATE/feature_request.yml
-    - .github/PULL_REQUEST_TEMPLATE.md
-    - .github/workflows/branch.yml
-    - .github/workflows/linting_comment.yml
-    - .github/workflows/linting.yml
-    - .github/CONTRIBUTING.md
-    - .github/.dockstore.yml
     - .github/CONTRIBUTING.md
     - .prettierignore
-    - .prettierignore
-    - .prettierignore
-    - .github/ISSUE_TEMPLATE/bug_report.yml
-    - .github/ISSUE_TEMPLATE/config.yml
-    - .github/ISSUE_TEMPLATE/feature_request.yml
-    - .github/PULL_REQUEST_TEMPLATE.md
-    - .github/workflows/branch.yml
-    - .github/workflows/linting_comment.yml
-    - .github/workflows/linting.yml
-    - .github/CONTRIBUTING.md
-    - .github/.dockstore.yml
-    - .github/CONTRIBUTING.md
-    - .prettierignore
-    - .prettierignore
-    - .prettierignore
     - CODE_OF_CONDUCT.md
     - assets/nf-core-longreadmag_logo_light.png
     - docs/images/nf-core-longreadmag_logo_light.png
     - docs/images/nf-core-longreadmag_logo_dark.png
     - .github/ISSUE_TEMPLATE/bug_report.yml
-  included_configs: false
+    - .github/workflows/branch.yml
+    - .github/workflows/linting_comment.yml
+    - .github/workflows/linting.yml
   multiqc_config:
     - report_comment
   nextflow_config:
@@ -77,10 +39,12 @@ lint:
     - validation.help.afterText
     - validation.summary.beforeText
     - validation.summary.afterText
+    - config_defaults:
+        - params.hmm_gtdb_pfam
+        - params.hmm_gtdb_tigrfam
+        - params.checkm2_db_version
   readme:
     - nextflow_badge
-    - nextflow_badge
-    - nextflow_badge
 nf_core_version: 3.0.2
 org_path: null
 repository_type: pipeline

.pre-commit-config.yaml

@@ -11,3 +11,4 @@ repos:
     hooks:
       - id: editorconfig-checker
         alias: ec
+        exclude: .*(\.hmm$|.*\.cm$)

.prettierignore

@@ -1,4 +1,5 @@
-
+adaptivecard.json
+slackreport.json
 .nextflow*
 work/
 data/

README.md

@@ -2,49 +2,53 @@
 
 ## Introduction
 
-**sanger-tol/longreadmag** is a bioinformatics pipeline that ...
-
-<!-- TODO nf-core:
-   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the
-   major pipeline sections and the types of output it produces. You're giving an overview to someone new
-   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction
--->
+**sanger-tol/longreadmag** is a bioinformatics pipeline for the assembly and binning of metagenomes
+using PacBio HiFi data and (optionally) Hi-C Illumina data.
 
 <!-- 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 -->
 
-2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+1. Assembles raw reads using metaMDBG ([`MultiQC`](http://multiqc.info/))
+2. Maps HiFi and (optionally) Hi-C reads to the assembly
+3. Bins the assembly using MetaBat2, MaxBin2, Bin3C, and Metator
+4. (optionally) refine the bins using DAS_Tool or MagScoT
+5. Assesses the completeness and contamination of bins using CheckM2 and assesses ncRNA content using tRNAscan-SE for tRNA and Infernal+Rfam for rRNA
+6. Assigns taxonomy to medium-quality and above bins using GTDB-Tk
+7. Summarises information at the bin level
 
 ## Usage
 
 > [!NOTE]
 > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
 
-<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
-     Explain what rows and columns represent. For instance (please edit as appropriate):
-
-First, prepare a samplesheet with your input data that looks as follows:
-
-`samplesheet.csv`:
-
-```csv
-sample,fastq_1,fastq_2
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
+First, prepare a YAML with your input data that looks as follows:
+
+`input.yaml`:
+
+```yaml
+id: SampleName
+pacbio:
+  fasta:
+    - /path/to/pacbio/file1.fasta.gz
+    - /path/to/pacbio/file2.fasta.gz
+    - ...
+hic:
+  cram:
+    - /path/to/hic/hic1.cram
+    - /path/to/hic/hic2.cram
+    - ...
+  enzymes:
+    - enzyme_name_1 (e.g. DpnII)
+    - enzyme_name_1 (e.g. HinfI)
+    - ...
 ```
 
-Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
-
--->
-
 Now, 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 sanger-tol/longreadmag \
    -profile <docker/singularity/.../institute> \
-   --input samplesheet.csv \
+   --input input.yaml \
    --outdir <OUTDIR>
 ```
 
@@ -55,9 +59,7 @@ nextflow run sanger-tol/longreadmag \
 
 sanger-tol/longreadmag was originally written by Jim Downie, Will Eagles, Noah Gettle.
 
-We thank the following people for their extensive assistance in the development of this pipeline:
-
-<!-- TODO nf-core: If applicable, make list of people who have also contributed -->
+<!-- We thank the following people for their extensive assistance in the development of this pipeline: -->
 
 ## Contributions and Support