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build: upgrade tool versions #155

Merged
merged 12 commits into from
Feb 3, 2024
Merged

build: upgrade tool versions #155

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27f4a6f
build: upgrade tool versions
uniqueg Feb 1, 2024
f8d72a3
Merge branch 'dev' into upgrade_tool_versions
uniqueg Feb 1, 2024
175e564
Merge branch 'dev' into upgrade_tool_versions
uniqueg Feb 2, 2024
12f7c9b
upgrade HTSinfer to 0.10.0
uniqueg Feb 2, 2024
b2d17c0
Merge branch 'upgrade_tool_versions' of github.com:zavolanlab/zarp in…
uniqueg Feb 2, 2024
25031d5
downgrade kallisto back to 0.46.2
uniqueg Feb 2, 2024
59b2685
bump kallisto to 0.48.0
uniqueg Feb 2, 2024
d311d2e
Merge branch 'dev' into upgrade_tool_versions
uniqueg Feb 2, 2024
f20d982
roll back source for htsinfer image
uniqueg Feb 2, 2024
7efba8f
update MD5 sums
uniqueg Feb 2, 2024
913385e
update MD5 sums
uniqueg Feb 2, 2024
6924b17
update MD5 sums; all test scripts executable
uniqueg Feb 3, 2024
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Empty file modified tests/test_format/test_snakefmt.sh
100644 → 100755
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Empty file modified tests/test_format/test_snakemake_lint.sh
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114 changes: 57 additions & 57 deletions tests/test_integration_workflow/expected_output.md5
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122 changes: 57 additions & 65 deletions tests/test_integration_workflow/expected_output_temp_flag.md5
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114 changes: 57 additions & 57 deletions tests/test_integration_workflow_multiple_lanes/expected_output.md5
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114 changes: 57 additions & 57 deletions tests/test_integration_workflow_with_conda/expected_output.md5
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Empty file modified tests/test_sra_download_with_conda/test.local.sh
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36 changes: 18 additions & 18 deletions workflow/Snakefile
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Expand Up @@ -207,7 +207,7 @@ rule start:
f"{current_rule}_{{sample}}.{{mate}}.stdout.log",
),
container:
"docker://ubuntu:focal-20210416"
"docker://ubuntu:jammy-20240111"
shell:
"(cat {input.reads} > {output.reads}) \
1> {log.stdout} 2> {log.stderr} "
Expand Down Expand Up @@ -243,7 +243,7 @@ rule fastqc:
resources:
mem_mb=lambda wildcards, attempt: 4096 * attempt,
container:
"docker://quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1"
"docker://quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0"
conda:
os.path.join(workflow.basedir, "envs", "fastqc.yaml")
log:
Expand Down Expand Up @@ -299,7 +299,7 @@ rule fastqc_trimmed:
),
threads: 1
container:
"docker://quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1"
"docker://quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0"
conda:
os.path.join(workflow.basedir, "envs", "fastqc.yaml")
log:
Expand Down Expand Up @@ -373,7 +373,7 @@ rule create_index_star:
),
),
container:
"docker://quay.io/biocontainers/star:2.7.8a--h9ee0642_1"
"docker://quay.io/biocontainers/star:2.7.11b--h43eeafb_0"
conda:
os.path.join(workflow.basedir, "envs", "STAR.yaml")
threads: 12
Expand Down Expand Up @@ -421,7 +421,7 @@ rule sort_gtf:
params:
cluster_log_path=config["cluster_log_dir"],
container:
"docker://ubuntu:focal-20210416"
"docker://ubuntu:jammy-20240111"
threads: 1
resources:
mem_mb=lambda wildcards, attempt: 32000 * attempt,
Expand Down Expand Up @@ -471,7 +471,7 @@ rule extract_transcriptome:
),
),
container:
"docker://quay.io/biocontainers/gffread:0.12.1--h2e03b76_1"
"docker://quay.io/biocontainers/gffread:0.12.7--hdcf5f25_3"
conda:
os.path.join(workflow.basedir, "envs", "gffread.yaml")
resources:
Expand Down Expand Up @@ -514,7 +514,7 @@ rule concatenate_transcriptome_and_genome:
params:
cluster_log_path=config["cluster_log_dir"],
container:
"docker://ubuntu:focal-20210416"
"docker://ubuntu:jammy-20240111"
resources:
mem_mb=lambda wildcards, attempt: 4096 * attempt,
log:
Expand Down Expand Up @@ -568,7 +568,7 @@ rule create_index_salmon:
),
),
container:
"docker://quay.io/biocontainers/salmon:1.4.0--h84f40af_1"
"docker://quay.io/biocontainers/salmon:1.10.2--hecfa306_0"
conda:
os.path.join(workflow.basedir, "envs", "salmon.yaml")
threads: 8
Expand Down Expand Up @@ -612,7 +612,7 @@ rule create_index_kallisto:
rule_config, current_rule=current_rule, immutable=("-i",)
),
container:
"docker://quay.io/biocontainers/kallisto:0.46.2--h60f4f9f_2"
"docker://quay.io/biocontainers/kallisto:0.48.0--h15996b6_2"
conda:
os.path.join(workflow.basedir, "envs", "kallisto.yaml")
resources:
Expand Down Expand Up @@ -662,7 +662,7 @@ rule extract_transcripts_as_bed12:
),
),
container:
"docker://quay.io/biocontainers/zgtf:0.1.1--pyh5e36f6f_0"
"docker://quay.io/biocontainers/zgtf:0.1.2--pyh5e36f6f_0"
conda:
os.path.join(workflow.basedir, "envs", "zgtf.yaml")
threads: 1
Expand Down Expand Up @@ -708,7 +708,7 @@ rule sort_genomic_alignment_samtools:
rule_config, current_rule=current_rule, immutable=()
),
container:
"docker://quay.io/biocontainers/samtools:1.9--h10a08f8_12"
"docker://quay.io/biocontainers/samtools:1.19.2--h50ea8bc_0"
conda:
os.path.join(workflow.basedir, "envs", "samtools.yaml")
threads: 8
Expand Down Expand Up @@ -765,7 +765,7 @@ rule index_genomic_alignment_samtools:
rule_config, current_rule=current_rule, immutable=()
),
container:
"docker://quay.io/biocontainers/samtools:1.3.1--h1b8c3c0_8"
"docker://quay.io/biocontainers/samtools:1.19.2--h50ea8bc_0"
conda:
os.path.join(workflow.basedir, "envs", "samtools.yaml")
threads: 1
Expand Down Expand Up @@ -930,7 +930,7 @@ rule salmon_quantmerge_genes:
),
),
container:
"docker://quay.io/biocontainers/salmon:1.4.0--h84f40af_1"
"docker://quay.io/biocontainers/salmon:1.10.2--hecfa306_0"
conda:
os.path.join(workflow.basedir, "envs", "salmon.yaml")
threads: 1
Expand Down Expand Up @@ -1017,7 +1017,7 @@ rule salmon_quantmerge_transcripts:
),
),
container:
"docker://quay.io/biocontainers/salmon:1.4.0--h84f40af_1"
"docker://quay.io/biocontainers/salmon:1.10.2--hecfa306_0"
conda:
os.path.join(workflow.basedir, "envs", "salmon.yaml")
threads: 1
Expand Down Expand Up @@ -1380,7 +1380,7 @@ rule star_rpm:
),
),
container:
"docker://quay.io/biocontainers/star:2.7.8a--h9ee0642_1"
"docker://quay.io/biocontainers/star:2.7.11b--h43eeafb_0"
conda:
os.path.join(workflow.basedir, "envs", "STAR.yaml")
threads: 4
Expand Down Expand Up @@ -1469,7 +1469,7 @@ rule rename_star_rpm_for_alfa:
params:
cluster_log_path=config["cluster_log_dir"],
container:
"docker://ubuntu:focal-20210416"
"docker://ubuntu:jammy-20240111"
log:
stderr=os.path.join(
config["log_dir"],
Expand Down Expand Up @@ -1902,7 +1902,7 @@ rule sort_bed_4_big:
rule_config, current_rule=current_rule, immutable=("-i",)
),
container:
"docker://quay.io/biocontainers/bedtools:2.27.1--h9a82719_5"
"docker://quay.io/biocontainers/bedtools:2.31.1--hf5e1c6e_0"
conda:
os.path.join(workflow.basedir, "envs", "bedtools.yaml")
resources:
Expand Down Expand Up @@ -1959,7 +1959,7 @@ rule prepare_bigWig:
rule_config, current_rule=current_rule, immutable=()
),
container:
"docker://quay.io/biocontainers/ucsc-bedgraphtobigwig:377--h0b8a92a_2"
"docker://quay.io/biocontainers/ucsc-bedgraphtobigwig:455--h2a80c09_0"
conda:
os.path.join(workflow.basedir, "envs", "ucsc-bedgraphtobigwig.yaml")
resources:
Expand Down
2 changes: 1 addition & 1 deletion workflow/envs/STAR.yaml
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Expand Up @@ -3,5 +3,5 @@ channels:
- conda-forge
- bioconda
dependencies:
- STAR=2.7.8a
- STAR=2.7.11b
...
2 changes: 1 addition & 1 deletion workflow/envs/bedtools.yaml
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Expand Up @@ -3,5 +3,5 @@ channels:
- conda-forge
- bioconda
dependencies:
- bedtools=2.27.1
- bedtools=2.31.1
...
2 changes: 1 addition & 1 deletion workflow/envs/fastqc.yaml
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Expand Up @@ -3,5 +3,5 @@ channels:
- conda-forge
- bioconda
dependencies:
- fastqc=0.11.9
- fastqc=0.12.1
...
2 changes: 1 addition & 1 deletion workflow/envs/gffread.yaml
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Expand Up @@ -3,5 +3,5 @@ channels:
- conda-forge
- bioconda
dependencies:
- gffread=0.12.1
- gffread=0.12.7
...
2 changes: 1 addition & 1 deletion workflow/envs/htsinfer.yaml
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Expand Up @@ -2,5 +2,5 @@
channels:
- bioconda
dependencies:
- htsinfer=0.9.0
- htsinfer=0.10.0
...
2 changes: 1 addition & 1 deletion workflow/envs/kallisto.yaml
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Expand Up @@ -3,5 +3,5 @@ channels:
- conda-forge
- bioconda
dependencies:
- kallisto=0.46.2
- kallisto=0.48.0
...
4 changes: 2 additions & 2 deletions workflow/envs/pigz.yaml
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Expand Up @@ -3,5 +3,5 @@ channels:
- conda-forge
- bioconda
dependencies:
- pigz=2.6
...
- pigz=2.8
...
2 changes: 1 addition & 1 deletion workflow/envs/salmon.yaml
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Expand Up @@ -3,5 +3,5 @@ channels:
- conda-forge
- bioconda
dependencies:
- salmon=1.4.0
- salmon=1.10.2
...
2 changes: 1 addition & 1 deletion workflow/envs/samtools.yaml
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Expand Up @@ -2,5 +2,5 @@
channels:
- bioconda
dependencies:
- samtools=1.9
- samtools=1.19.2
...
4 changes: 2 additions & 2 deletions workflow/envs/sra-tools.yaml
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Expand Up @@ -3,5 +3,5 @@ channels:
- conda-forge
- bioconda
dependencies:
- sra-tools=2.11.0
...
- sra-tools=3.0.10
...
2 changes: 1 addition & 1 deletion workflow/envs/ucsc-bedgraphtobigwig.yaml
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Expand Up @@ -3,5 +3,5 @@ channels:
- conda-forge
- bioconda
dependencies:
- ucsc-bedgraphtobigwig=377
- ucsc-bedgraphtobigwig=455
...
2 changes: 1 addition & 1 deletion workflow/envs/zgtf.yaml
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Expand Up @@ -3,5 +3,5 @@ channels:
- conda-forge
- bioconda
dependencies:
- zgtf=0.1.1
- zgtf=0.1.2
...
8 changes: 4 additions & 4 deletions workflow/rules/paired_end.snakefile.smk
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Expand Up @@ -157,7 +157,7 @@ rule pe_remove_polya_cutadapt:
),
),
container:
"docker://quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1"
"docker://quay.io/biocontainers/cutadapt:4.6--py310h4b81fae_1"
conda:
os.path.join(workflow.basedir, "envs", "cutadapt.yaml")
threads: 4
Expand Down Expand Up @@ -263,7 +263,7 @@ rule pe_map_genome_star:
),
),
container:
"docker://quay.io/biocontainers/star:2.7.8a--h9ee0642_1"
"docker://quay.io/biocontainers/star:2.7.11b--h43eeafb_0"
conda:
os.path.join(workflow.basedir, "envs", "STAR.yaml")
threads: 12
Expand Down Expand Up @@ -374,7 +374,7 @@ rule pe_quantification_salmon:
),
),
container:
"docker://quay.io/biocontainers/salmon:1.4.0--h84f40af_1"
"docker://quay.io/biocontainers/salmon:1.10.2--hecfa306_0"
conda:
os.path.join(workflow.basedir, "envs", "salmon.yaml")
threads: 6
Expand Down Expand Up @@ -464,7 +464,7 @@ rule pe_genome_quantification_kallisto:
),
),
container:
"docker://quay.io/biocontainers/kallisto:0.46.2--h60f4f9f_2"
"docker://quay.io/biocontainers/kallisto:0.48.0--h15996b6_2"
conda:
os.path.join(workflow.basedir, "envs", "kallisto.yaml")
threads: 8
Expand Down
8 changes: 4 additions & 4 deletions workflow/rules/single_end.snakefile.smk
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Expand Up @@ -43,7 +43,7 @@ rule remove_adapters_cutadapt:
),
),
container:
"docker://quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1"
"docker://quay.io/biocontainers/cutadapt:4.6--py310h4b81fae_1"
conda:
os.path.join(workflow.basedir, "envs", "cutadapt.yaml")
threads: 4
Expand Down Expand Up @@ -208,7 +208,7 @@ rule map_genome_star:
),
),
container:
"docker://quay.io/biocontainers/star:2.7.8a--h9ee0642_1"
"docker://quay.io/biocontainers/star:2.7.11b--h43eeafb_0"
conda:
os.path.join(workflow.basedir, "envs", "STAR.yaml")
threads: 12
Expand Down Expand Up @@ -318,7 +318,7 @@ rule quantification_salmon:
),
),
container:
"docker://quay.io/biocontainers/salmon:1.4.0--h84f40af_1"
"docker://quay.io/biocontainers/salmon:1.10.2--hecfa306_0"
conda:
os.path.join(workflow.basedir, "envs", "salmon.yaml")
threads: 6
Expand Down Expand Up @@ -409,7 +409,7 @@ rule genome_quantification_kallisto:
),
),
container:
"docker://quay.io/biocontainers/kallisto:0.46.2--h60f4f9f_2"
"docker://quay.io/biocontainers/kallisto:0.48.0--h15996b6_2"
conda:
os.path.join(workflow.basedir, "envs", "kallisto.yaml")
threads: 8
Expand Down
6 changes: 3 additions & 3 deletions workflow/rules/sra_download.smk
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Expand Up @@ -30,7 +30,7 @@ rule prefetch:
conda:
os.path.join(workflow.basedir, "..", "envs", "sra-tools.yaml")
singularity:
"docker://ncbi/sra-tools"
"docker://quay.io/biocontainers/sra-tools:3.0.10--h9f5acd7_0"
log:
stderr=os.path.join(
config["log_dir"], "samples", "{sample}", "prefetch.stderr.log"
Expand Down Expand Up @@ -61,7 +61,7 @@ checkpoint fasterq_dump:
conda:
os.path.join(workflow.basedir, "..", "envs", "sra-tools.yaml")
singularity:
"docker://ncbi/sra-tools"
"docker://quay.io/biocontainers/sra-tools:3.0.10--h9f5acd7_0"
log:
stderr=os.path.join(
config["log_dir"], "samples", "{sample}", "fasterq_dump.stderr.log"
Expand Down Expand Up @@ -111,7 +111,7 @@ rule compress_fastq:
conda:
os.path.join(workflow.basedir, "..", "envs", "pigz.yaml")
singularity:
"docker://bytesco/pigz"
"docker://quay.io/biocontainers/pigz:2.8"
log:
stderr=os.path.join(
config["log_dir"], "samples", "{sample}", "compress_fastq.stderr.log"
Expand Down
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