Skip to content

Commit 08fad68

Browse files
github-actions[bot]github-actions[bot]
committed
Update lint results [skip ci]
1 parent 15b3c5a commit 08fad68

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

49 files changed

+98
-1431
lines changed

‎README.md‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -12,13 +12,13 @@ The goal is for all sanger-tol pipelines to run without errors using strict synt
1212
> See the [nf-core blog post](https://nf-co.re/blog/2025/nextflow_syntax_nf-core_roadmap) for details on the migration timeline.
1313
> **Fixing all errors from `nextflow lint` will be a requirement by early spring 2026.**
1414
15-
- **Last updated:** 2026-02-20 00:10:28 UTC
15+
- **Last updated:** 2026-02-21 00:08:46 UTC
1616
- **Nextflow version:** 26.01.1-edge
1717

1818
## Pipelines
1919

20-
- **Total:** 0 parse errors, 101 errors, 366 warnings across 19 pipelines
21-
- **Zero errors:** 14 pipelines (73.7%)
20+
- **Total:** 0 parse errors, 80 errors, 190 warnings across 19 pipelines
21+
- **Zero errors:** 15 pipelines (78.9%)
2222

2323
| Errors | Warnings |
2424
| :------------------------------------------: | :----------------------------------------------: |
@@ -30,7 +30,6 @@ The goal is for all sanger-tol pipelines to run without errors using strict synt
3030
| Pipeline | Parse Error | Errors | Warnings | Prints Help | Lint Output | Help Output |
3131
| ----------------------------------------------------------------------------------------------- | :---------: | -----: | -------: | :---------: | :-----------------------------------------------------------------: | :---------------------------------------------------------------------: |
3232
| :x: [genealignment](https://github.com/sanger-tol/genealignment) | No | 61 | 28 | - | [View](lint_results/pipeline-results/genealignment_lint.md) | - |
33-
| :x: [treeval](https://github.com/sanger-tol/treeval) | No | 21 | 177 | - | [View](lint_results/pipeline-results/treeval_lint.md) | - |
3433
| :x: [curationpretext](https://github.com/sanger-tol/curationpretext) | No | 13 | 53 | - | [View](lint_results/pipeline-results/curationpretext_lint.md) | - |
3534
| :x: [zippypretext](https://github.com/sanger-tol/zippypretext) | No | 5 | 15 | - | [View](lint_results/pipeline-results/zippypretext_lint.md) | - |
3635
| :x: [ascc](https://github.com/sanger-tol/ascc) | No | 1 | 7 | - | [View](lint_results/pipeline-results/ascc_lint.md) | - |
@@ -39,6 +38,7 @@ The goal is for all sanger-tol pipelines to run without errors using strict synt
3938
| :white_check_mark: [blobtoolkit](https://github.com/sanger-tol/blobtoolkit) | No | 0 | 7 | Yes | [View](lint_results/pipeline-results/blobtoolkit_lint.md) | [View](lint_results/prints-help-results/blobtoolkit_help.txt) |
4039
| :x: [purging](https://github.com/sanger-tol/purging) | No | 0 | 5 | No | [View](lint_results/pipeline-results/purging_lint.md) | [View](lint_results/prints-help-results/purging_help.txt) |
4140
| :white_check_mark: [genomeassembly](https://github.com/sanger-tol/genomeassembly) | No | 0 | 1 | Yes | [View](lint_results/pipeline-results/genomeassembly_lint.md) | [View](lint_results/prints-help-results/genomeassembly_help.txt) |
41+
| :x: [treeval](https://github.com/sanger-tol/treeval) | No | 0 | 1 | No | [View](lint_results/pipeline-results/treeval_lint.md) | [View](lint_results/prints-help-results/treeval_help.txt) |
4242
| :white_check_mark: [ensemblgenedownload](https://github.com/sanger-tol/ensemblgenedownload) | No | 0 | 0 | Yes | [View](lint_results/pipeline-results/ensemblgenedownload_lint.md) | [View](lint_results/prints-help-results/ensemblgenedownload_help.txt) |
4343
| :white_check_mark: [ensemblrepeatdownload](https://github.com/sanger-tol/ensemblrepeatdownload) | No | 0 | 0 | Yes | [View](lint_results/pipeline-results/ensemblrepeatdownload_lint.md) | [View](lint_results/prints-help-results/ensemblrepeatdownload_help.txt) |
4444
| :white_check_mark: [genomenote](https://github.com/sanger-tol/genomenote) | No | 0 | 0 | Yes | [View](lint_results/pipeline-results/genomenote_lint.md) | [View](lint_results/prints-help-results/genomenote_help.txt) |

‎lint_results/module-results/ancestral_extract_lint.md‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
# Nextflow lint results
22

3-
- Generated: 2026-02-20T00:10:04.460466+00:00
3+
- Generated: 2026-02-21T00:08:33.042326+00:00
44
- Nextflow version: 26.01.1-edge
55
- Summary: No issues found

‎lint_results/module-results/ancestral_plot_lint.md‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
# Nextflow lint results
22

3-
- Generated: 2026-02-20T00:10:04.460634+00:00
3+
- Generated: 2026-02-21T00:08:33.042488+00:00
44
- Nextflow version: 26.01.1-edge
55
- Summary: No issues found

‎lint_results/module-results/bedchunks_create_lint.md‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
# Nextflow lint results
22

3-
- Generated: 2026-02-20T00:10:04.460748+00:00
3+
- Generated: 2026-02-21T00:08:33.042601+00:00
44
- Nextflow version: 26.01.1-edge
55
- Summary: No issues found

‎lint_results/module-results/bedtools_bamtobedsort_lint.md‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
# Nextflow lint results
22

3-
- Generated: 2026-02-20T00:10:04.460875+00:00
3+
- Generated: 2026-02-21T00:08:33.042706+00:00
44
- Nextflow version: 26.01.1-edge
55
- Summary: No issues found

‎lint_results/module-results/blast_blastn_lint.md‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
# Nextflow lint results
22

3-
- Generated: 2026-02-20T00:10:04.460991+00:00
3+
- Generated: 2026-02-21T00:08:33.042807+00:00
44
- Nextflow version: 26.01.1-edge
55
- Summary: No issues found

‎lint_results/module-results/blobtoolkit_generatecsv_lint.md‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
# Nextflow lint results
22

3-
- Generated: 2026-02-20T00:10:04.461105+00:00
3+
- Generated: 2026-02-21T00:08:33.042905+00:00
44
- Nextflow version: 26.01.1-edge
55
- Summary: No issues found

‎lint_results/module-results/blobtoolkit_generateparamsfile_lint.md‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
# Nextflow lint results
22

3-
- Generated: 2026-02-20T00:10:04.461264+00:00
3+
- Generated: 2026-02-21T00:08:33.043041+00:00
44
- Nextflow version: 26.01.1-edge
55
- Summary: No issues found

‎lint_results/module-results/cramalign_bwamem2alignhic_lint.md‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
# Nextflow lint results
22

3-
- Generated: 2026-02-20T00:10:04.461398+00:00
3+
- Generated: 2026-02-21T00:08:33.043151+00:00
44
- Nextflow version: 26.01.1-edge
55
- Summary: No issues found

‎lint_results/module-results/cramalign_gencramchunks_lint.md‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
# Nextflow lint results
22

3-
- Generated: 2026-02-20T00:10:04.461525+00:00
3+
- Generated: 2026-02-21T00:08:33.043249+00:00
44
- Nextflow version: 26.01.1-edge
55
- Summary: No issues found

0 commit comments

Comments
 (0)