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restore samtools modules version bump #6685

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merged 3 commits into from
Sep 24, 2024
Merged

restore samtools modules version bump #6685

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d94a970
restore samtools modules version bump
maxulysse Sep 24, 2024
97da435
add htslib
maxulysse Sep 24, 2024
0165878
same environment.yml file for each samtools modules
maxulysse Sep 24, 2024
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7 changes: 4 additions & 3 deletions modules/nf-core/samtools/ampliconclip/environment.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.20
- bioconda::samtools=1.20
- bioconda::htslib=1.21
- bioconda::samtools=1.21
7 changes: 4 additions & 3 deletions modules/nf-core/samtools/bam2fq/environment.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.20
- bioconda::samtools=1.20
- bioconda::htslib=1.21
- bioconda::samtools=1.21
7 changes: 4 additions & 3 deletions modules/nf-core/samtools/calmd/environment.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.20
- bioconda::samtools=1.20
- bioconda::htslib=1.21
- bioconda::samtools=1.21
7 changes: 4 additions & 3 deletions modules/nf-core/samtools/cat/environment.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.20
- bioconda::samtools=1.20
- bioconda::htslib=1.21
- bioconda::samtools=1.21
7 changes: 4 additions & 3 deletions modules/nf-core/samtools/collate/environment.yml
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@@ -1,7 +1,8 @@
---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.20
- bioconda::samtools=1.20
- bioconda::htslib=1.21
- bioconda::samtools=1.21
7 changes: 4 additions & 3 deletions modules/nf-core/samtools/collatefastq/environment.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.20
- bioconda::samtools=1.20
- bioconda::htslib=1.21
- bioconda::samtools=1.21
3 changes: 2 additions & 1 deletion modules/nf-core/samtools/consensus/environment.yml
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Expand Up @@ -4,4 +4,5 @@ channels:
- conda-forge
- bioconda
dependencies:
- "bioconda::samtools=1.20"
- bioconda::htslib=1.21
- bioconda::samtools=1.21
7 changes: 4 additions & 3 deletions modules/nf-core/samtools/convert/environment.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.20
- bioconda::samtools=1.20
- bioconda::htslib=1.21
- bioconda::samtools=1.21
7 changes: 4 additions & 3 deletions modules/nf-core/samtools/coverage/environment.yml
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@@ -1,7 +1,8 @@
---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.20
- bioconda::samtools=1.20
- bioconda::htslib=1.21
- bioconda::samtools=1.21
3 changes: 2 additions & 1 deletion modules/nf-core/samtools/cramsize/environment.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.21
- bioconda::samtools=1.21
7 changes: 4 additions & 3 deletions modules/nf-core/samtools/depth/environment.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.20
- bioconda::samtools=1.20
- bioconda::htslib=1.21
- bioconda::samtools=1.21
7 changes: 4 additions & 3 deletions modules/nf-core/samtools/dict/environment.yml
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@@ -1,7 +1,8 @@
---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.20
- bioconda::samtools=1.20
- bioconda::htslib=1.21
- bioconda::samtools=1.21
3 changes: 2 additions & 1 deletion modules/nf-core/samtools/faidx/environment.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.21
- bioconda::samtools=1.21
7 changes: 4 additions & 3 deletions modules/nf-core/samtools/fasta/environment.yml
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@@ -1,7 +1,8 @@
---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.20
- bioconda::samtools=1.20
- bioconda::htslib=1.21
- bioconda::samtools=1.21
7 changes: 4 additions & 3 deletions modules/nf-core/samtools/fastq/environment.yml
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@@ -1,7 +1,8 @@
---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.20
- bioconda::samtools=1.20
- bioconda::htslib=1.21
- bioconda::samtools=1.21
7 changes: 4 additions & 3 deletions modules/nf-core/samtools/fixmate/environment.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.20
- bioconda::samtools=1.20
- bioconda::htslib=1.21
- bioconda::samtools=1.21
7 changes: 4 additions & 3 deletions modules/nf-core/samtools/flagstat/environment.yml
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@@ -1,7 +1,8 @@
---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.20
- bioconda::samtools=1.20
- bioconda::htslib=1.21
- bioconda::samtools=1.21
7 changes: 4 additions & 3 deletions modules/nf-core/samtools/getrg/environment.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.20
- bioconda::samtools=1.20
- bioconda::htslib=1.21
- bioconda::samtools=1.21
7 changes: 4 additions & 3 deletions modules/nf-core/samtools/idxstats/environment.yml
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@@ -1,7 +1,8 @@
---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.20
- bioconda::samtools=1.20
- bioconda::htslib=1.21
- bioconda::samtools=1.21
7 changes: 4 additions & 3 deletions modules/nf-core/samtools/import/environment.yml
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@@ -1,7 +1,8 @@
---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.20
- bioconda::samtools=1.20
- bioconda::htslib=1.21
- bioconda::samtools=1.21
7 changes: 4 additions & 3 deletions modules/nf-core/samtools/index/environment.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.20
- bioconda::samtools=1.20
- bioconda::htslib=1.21
- bioconda::samtools=1.21
7 changes: 4 additions & 3 deletions modules/nf-core/samtools/markdup/environment.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.20
- bioconda::samtools=1.20
- bioconda::htslib=1.21
- bioconda::samtools=1.21
7 changes: 4 additions & 3 deletions modules/nf-core/samtools/merge/environment.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.20
- bioconda::samtools=1.20
- bioconda::htslib=1.21
- bioconda::samtools=1.21
7 changes: 4 additions & 3 deletions modules/nf-core/samtools/mpileup/environment.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.20
- bioconda::samtools=1.20
- bioconda::htslib=1.21
- bioconda::samtools=1.21
7 changes: 4 additions & 3 deletions modules/nf-core/samtools/reheader/environment.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.20
- bioconda::samtools=1.20
- bioconda::htslib=1.21
- bioconda::samtools=1.21
7 changes: 4 additions & 3 deletions modules/nf-core/samtools/sormadup/environment.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.20
- bioconda::samtools=1.20
- bioconda::htslib=1.21
- bioconda::samtools=1.21
7 changes: 4 additions & 3 deletions modules/nf-core/samtools/sort/environment.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.20
- bioconda::samtools=1.20
- bioconda::htslib=1.21
- bioconda::samtools=1.21
7 changes: 4 additions & 3 deletions modules/nf-core/samtools/stats/environment.yml
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@@ -1,7 +1,8 @@
---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.20
- bioconda::samtools=1.20
- bioconda::htslib=1.21
- bioconda::samtools=1.21
7 changes: 4 additions & 3 deletions modules/nf-core/samtools/view/environment.yml
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@@ -1,7 +1,8 @@
---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.20
- bioconda::samtools=1.20
- bioconda::htslib=1.21
- bioconda::samtools=1.21
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