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FASTQREPAIR first release #2

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5f52cb7
raw setup of the pipeline
mazzalab Oct 1, 2024
b3b5752
Optionally run trimmomatic and bbmap on paired-reads only
mazzalab Oct 2, 2024
bc96d04
samplesheet check added - multiple runs of same fastq not allowed
mazzalab Oct 2, 2024
83b7d48
README filled. Check fastq replicas unstable
mazzalab Oct 11, 2024
d9aaac4
fixed check of multiple identical fastq files which are forbitten
mazzalab Oct 11, 2024
90fe11a
added fastqc and added biblio references
mazzalab Oct 12, 2024
b978dd0
renamer module added for final files renaming and read chunks fix
mazzalab Oct 13, 2024
50ae8be
tests added and starrt documenting and resolving TODOs
mazzalab Oct 20, 2024
90a50e8
dataset removed
mazzalab Oct 20, 2024
96a07c2
Template update for nf-core/tools version 3.0.2
mazzalab Oct 20, 2024
3f0cb22
Merge branch 'TEMPLATE' into dev
mazzalab Oct 20, 2024
d211c2f
fixing post template-merge
mazzalab Oct 20, 2024
b67f40b
fixed gitignore file
mazzalab Oct 20, 2024
9d9c030
Fixed modules structure and renamed WIPER reports
mazzalab Oct 20, 2024
8924206
documentation done
mazzalab Oct 23, 2024
039b665
documentation done
mazzalab Oct 23, 2024
e5a0772
annotation done
mazzalab Oct 23, 2024
ca5e78e
fixed trailing whitespaces
mazzalab Oct 24, 2024
4106d10
fixing traling shitespaces
mazzalab Oct 24, 2024
1e054b0
run prettier on MD files
mazzalab Oct 24, 2024
8ab07f7
fixed the remaining TODOs
mazzalab Oct 24, 2024
ecbd2e3
updated local test files
mazzalab Oct 24, 2024
ffd6ba2
removed working files
mazzalab Oct 24, 2024
6180b60
Updated markdown files and NF schema
mazzalab Oct 26, 2024
c3bf750
match template
mazzalab Oct 26, 2024
07f1f7d
Fixed linting messages
mazzalab Oct 26, 2024
e5060bc
test linting online
mazzalab Oct 26, 2024
e53c867
trying to fix linting
mashehu Oct 27, 2024
70c26f7
[automated] Fix code linting
nf-core-bot Oct 27, 2024
9981e61
reply to @mashehu review
mazzalab Oct 27, 2024
a03a022
[automated] Fix code linting
nf-core-bot Oct 27, 2024
6850b9c
Fixed linting errors when images do not match the template
mazzalab Oct 27, 2024
af70eef
Merge pull request #1 from mazzalab/dev
mazzalab Oct 27, 2024
6325e69
fix linting
mashehu Oct 28, 2024
7fbaf48
Update CHANGELOG.md
mazzalab Oct 28, 2024
6389825
Reply @sateeshperi review. Still missing local modules tests
mazzalab Oct 28, 2024
d4a97e9
Improved properties descriptions in schema and README.md
mazzalab Oct 29, 2024
55e5a02
[automated] Fix code linting
nf-core-bot Oct 29, 2024
dff4907
improve code formatting
mazzalab Oct 29, 2024
6dde1ad
first batch of answers (the simplest to answer) to the review
mazzalab Oct 30, 2024
aa7753b
Fixed Put devcontainer configuration file back #5
mazzalab Nov 1, 2024
cb65430
Added the new nf-module gzrt. It closes gzrt as a module #7
mazzalab Dec 10, 2024
4ebd179
Template update for nf-core/tools version 3.1.0
nf-core-bot Dec 12, 2024
d6b229d
Fix #5
mazzalab Dec 15, 2024
8f5d34f
Merge branch 'TEMPLATE' of https://github.com/nf-core/fastqrepair int…
mazzalab Dec 15, 2024
2acab76
merging template changes
mazzalab Dec 15, 2024
538993a
Fixing linting and pre-commit errors
mazzalab Dec 15, 2024
978ec34
Fixing linting errors
mazzalab Dec 15, 2024
64e9c54
Comment unstable code to be fixed in dev
mazzalab Dec 15, 2024
34e7047
Comment out unstable code to be fixed in dev
mazzalab Dec 15, 2024
8a5cf11
Edit temporary tests
mazzalab Dec 15, 2024
95c73d8
samplesheet ext missing
mazzalab Dec 15, 2024
4f1cd89
updated gzrt module and commented the whole logics
mazzalab Dec 16, 2024
88998d8
Reverted manual edit in FASTQC module
mazzalab Dec 16, 2024
9762fca
Revert manual edits FastQC
mazzalab Dec 16, 2024
65cb7c5
fixing template errors
mazzalab Dec 16, 2024
531745e
fixing linting issues
mazzalab Dec 16, 2024
8a30713
fixing further linting issues
mazzalab Dec 16, 2024
ef54a84
Merge pull request #10 from mazzalab/merging-template-updates
mazzalab Dec 16, 2024
0802ee6
enabled a pipeline-specific nf-core config
mazzalab Dec 16, 2024
e64839d
Template update for nf-core/tools version 3.1.0
nf-core-bot Dec 20, 2024
b082bc1
Template update for nf-core/tools version 3.1.1
nf-core-bot Dec 20, 2024
18d3dc8
tiny changes irrelevant
mazzalab Dec 22, 2024
f0efee8
Merge branch 'dev' into nf-core-template-merge-3.1.1
mazzalab Dec 22, 2024
2a5a74e
Merge pull request #13 from nf-core/nf-core-template-merge-3.1.1
mazzalab Dec 22, 2024
0f6abd7
Update README.md
mazzalab Dec 22, 2024
2e0b602
Add new environment configurations and update dependencies for bbmap …
mazzalab Jan 8, 2025
8d6cf97
Remove Trimmomatic module and associated test configurations; update …
mazzalab Jan 12, 2025
0805d61
[automated] Fix code linting
nf-core-bot Jan 12, 2025
87b2da5
Updated flow diagram and README.md
tm4zza Jan 14, 2025
f6ca0ad
improved flow diagram and edited usage.md
tm4zza Jan 14, 2025
46540c3
Removed green box from the flow diagram
tm4zza Jan 14, 2025
2923b0f
Update .gitignore, add multiqc tags, and modify environment configura…
mazzalab Jan 14, 2025
26fe0d9
Update contributing guidelines, issue and pull request templates, and…
mazzalab Jan 14, 2025
6fb1678
Update contributing guidelines, issue templates, and workflows for cl…
mazzalab Jan 14, 2025
e1b7689
fixed linting problems with prettier
mazzalab Jan 14, 2025
4d75bcd
added new line at the end
mazzalab Jan 14, 2025
c0a9419
Fixed unchanged files
mazzalab Jan 15, 2025
6370f33
Add MultiQC configuration options and update WIPERTOOLS parameters
mazzalab Jan 15, 2025
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Improved properties descriptions in schema and README.md
mazzalab committed Oct 29, 2024

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commit d4a97e9287997ba072bbe08101514de3b25da0b0
2 changes: 1 addition & 1 deletion README.md
Original file line number Diff line number Diff line change
@@ -52,7 +52,7 @@ Now, you can run the pipeline using:

```bash
nextflow run nf-core/fastqrepair \
-profile <test/docker> \
-profile <test/docker/singularity/.../institute> \
--input samplesheet.csv \
--outdir <OUTDIR>
```
21 changes: 18 additions & 3 deletions nextflow_schema.json
Original file line number Diff line number Diff line change
@@ -10,7 +10,10 @@
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": ["input", "outdir"],
"required": [
"input",
"outdir"
],
"properties": {
"input": {
"type": "string",
@@ -38,7 +41,10 @@
},
"qin": {
"type": "integer",
"enum": [33, 64],
"enum": [
33,
64
],
"default": 33,
"description": "the ASCII offset (33=Sanger, 64=old Solexa).",
"fa_icon": "fas fa-puzzle-piece"
@@ -47,6 +53,7 @@
"type": "string",
"default": "ACGTN",
"description": "Allowed character in the SEQ line.",
"help_text": "SEQ lines containing characters not listed here will be discarded",
"fa_icon": "fas fa-solid fa-arrows-left-right-to-line"
},
"email": {
@@ -125,11 +132,19 @@
"description": "Method used to save pipeline results to output directory.",
"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
"fa_icon": "fas fa-copy",
"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
"enum": [
"symlink",
"rellink",
"link",
"copy",
"copyNoFollow",
"move"
],
"hidden": true
},
"publish_dir_all_tools": {
"type": "boolean",
"default": false,
"description": "To specify whether to publish all pipeline intermediate results to output directory.",
"help_text": "This option tells the pipeline whether to publish all intermediate results to output directory.",
"fa_icon": "fas fa-copy",