From b18c60ad7959ceef9f78f7731e29cc79ab8559ff Mon Sep 17 00:00:00 2001 From: Friederike Hanssen Date: Tue, 10 Dec 2024 12:52:58 +0100 Subject: [PATCH 1/2] Update docs/usage.md --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index d4f9f2c1c7..0a279cd6c5 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -585,7 +585,7 @@ This list is by no means exhaustive and it will depend on the specific analysis | [mpileup](https://www.htslib.org/doc/samtools-mpileup.html) | x | x | x | x | x | - | | [Strelka](https://github.com/Illumina/strelka) | x | x | x | x | - | x | | [Manta](https://github.com/Illumina/manta) | x | x | x | x | x | x | -| [indexcov](https://github.com/brentp/goleft/tree/master/indexcov) | x | - | x | x | x | x | +| [indexcov](https://github.com/brentp/goleft/tree/master/indexcov) | x | - | - | x | - | x | | [TIDDIT](https://github.com/SciLifeLab/TIDDIT) | x | x | x | x | x | x | | [ASCAT](https://github.com/VanLoo-lab/ascat) | x | x | - | - | - | x | | [CNVKit](https://cnvkit.readthedocs.io/en/stable/) | x | x | - | x | x | x | From b5b2ae2f3a869bd97a7b301f8d09b1bd6283eb66 Mon Sep 17 00:00:00 2001 From: Friederike Hanssen Date: Tue, 10 Dec 2024 12:58:55 +0100 Subject: [PATCH 2/2] Update modules/local/samtools/reindex_bam/environment.yml Co-authored-by: Maxime U Garcia --- modules/local/samtools/reindex_bam/environment.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/modules/local/samtools/reindex_bam/environment.yml b/modules/local/samtools/reindex_bam/environment.yml index e8488d1477..da2df5e43a 100644 --- a/modules/local/samtools/reindex_bam/environment.yml +++ b/modules/local/samtools/reindex_bam/environment.yml @@ -1,4 +1,3 @@ -name: samtools_view channels: - conda-forge - bioconda