From 27f4a6f96df04b38977d7e507747b47ec17b859d Mon Sep 17 00:00:00 2001 From: Alex Kanitz Date: Thu, 1 Feb 2024 14:36:58 +0100 Subject: [PATCH 1/8] build: upgrade tool versions --- workflow/Snakefile | 37 ++++++++++++------------ workflow/envs/STAR.yaml | 2 +- workflow/envs/bedtools.yaml | 2 +- workflow/envs/cutadapt.yaml | 2 +- workflow/envs/fastqc.yaml | 2 +- workflow/envs/gffread.yaml | 2 +- workflow/envs/kallisto.yaml | 2 +- workflow/envs/pigz.yaml | 4 +-- workflow/envs/salmon.yaml | 2 +- workflow/envs/samtools.yaml | 2 +- workflow/envs/sra-tools.yaml | 4 +-- workflow/envs/ucsc-bedgraphtobigwig.yaml | 2 +- workflow/envs/zgtf.yaml | 2 +- workflow/rules/htsinfer.smk | 4 +-- workflow/rules/paired_end.snakefile.smk | 10 +++---- workflow/rules/single_end.snakefile.smk | 10 +++---- workflow/rules/sra_download.smk | 6 ++-- 17 files changed, 48 insertions(+), 47 deletions(-) diff --git a/workflow/Snakefile b/workflow/Snakefile index 9f8f1ca..d75ad90 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -1,4 +1,5 @@ """General purpose RNA-Seq analysis pipeline developed by the Zavolan Lab""" + import os import pandas as pd import shutil @@ -206,7 +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} " @@ -242,7 +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: @@ -298,7 +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: @@ -372,7 +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 @@ -420,7 +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, @@ -470,7 +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: @@ -513,7 +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: @@ -567,7 +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 @@ -611,7 +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:0.50.1--hc877fd6_0" conda: os.path.join(workflow.basedir, "envs", "kallisto.yaml") resources: @@ -661,7 +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 @@ -707,7 +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 @@ -764,7 +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 @@ -929,7 +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 @@ -1016,7 +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 @@ -1379,7 +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 @@ -1468,7 +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"], @@ -1901,7 +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: @@ -1958,7 +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: diff --git a/workflow/envs/STAR.yaml b/workflow/envs/STAR.yaml index 4c4b622..441cae4 100644 --- a/workflow/envs/STAR.yaml +++ b/workflow/envs/STAR.yaml @@ -3,5 +3,5 @@ channels: - conda-forge - bioconda dependencies: - - STAR=2.7.8a + - STAR=2.7.11b ... diff --git a/workflow/envs/bedtools.yaml b/workflow/envs/bedtools.yaml index 2d40771..7694e7c 100644 --- a/workflow/envs/bedtools.yaml +++ b/workflow/envs/bedtools.yaml @@ -3,5 +3,5 @@ channels: - conda-forge - bioconda dependencies: - - bedtools=2.27.1 + - bedtools=2.31.1 ... diff --git a/workflow/envs/cutadapt.yaml b/workflow/envs/cutadapt.yaml index 064d302..4a42250 100644 --- a/workflow/envs/cutadapt.yaml +++ b/workflow/envs/cutadapt.yaml @@ -3,5 +3,5 @@ channels: - conda-forge - bioconda dependencies: - - cutadapt=3.4 + - cutadapt=4.6 ... diff --git a/workflow/envs/fastqc.yaml b/workflow/envs/fastqc.yaml index a5d96ff..b485019 100644 --- a/workflow/envs/fastqc.yaml +++ b/workflow/envs/fastqc.yaml @@ -3,5 +3,5 @@ channels: - conda-forge - bioconda dependencies: - - fastqc=0.11.9 + - fastqc=0.12.1 ... diff --git a/workflow/envs/gffread.yaml b/workflow/envs/gffread.yaml index 3b1399c..662cdaf 100644 --- a/workflow/envs/gffread.yaml +++ b/workflow/envs/gffread.yaml @@ -3,5 +3,5 @@ channels: - conda-forge - bioconda dependencies: - - gffread=0.12.1 + - gffread=0.12.7 ... diff --git a/workflow/envs/kallisto.yaml b/workflow/envs/kallisto.yaml index 977d1cd..f928bb2 100644 --- a/workflow/envs/kallisto.yaml +++ b/workflow/envs/kallisto.yaml @@ -3,5 +3,5 @@ channels: - conda-forge - bioconda dependencies: - - kallisto=0.46.2 + - kallisto=0.50.1 ... diff --git a/workflow/envs/pigz.yaml b/workflow/envs/pigz.yaml index 692cf20..c0ef351 100644 --- a/workflow/envs/pigz.yaml +++ b/workflow/envs/pigz.yaml @@ -3,5 +3,5 @@ channels: - conda-forge - bioconda dependencies: - - pigz=2.6 -... \ No newline at end of file + - pigz=2.8 +... diff --git a/workflow/envs/salmon.yaml b/workflow/envs/salmon.yaml index 9db5f9d..0101c9e 100644 --- a/workflow/envs/salmon.yaml +++ b/workflow/envs/salmon.yaml @@ -3,5 +3,5 @@ channels: - conda-forge - bioconda dependencies: - - salmon=1.4.0 + - salmon=1.10.2 ... diff --git a/workflow/envs/samtools.yaml b/workflow/envs/samtools.yaml index 58a35ed..e1478a1 100644 --- a/workflow/envs/samtools.yaml +++ b/workflow/envs/samtools.yaml @@ -2,5 +2,5 @@ channels: - bioconda dependencies: - - samtools=1.9 + - samtools=1.19.2 ... diff --git a/workflow/envs/sra-tools.yaml b/workflow/envs/sra-tools.yaml index 5811bcf..ed9556f 100644 --- a/workflow/envs/sra-tools.yaml +++ b/workflow/envs/sra-tools.yaml @@ -3,5 +3,5 @@ channels: - conda-forge - bioconda dependencies: - - sra-tools=2.11.0 -... \ No newline at end of file + - sra-tools=3.0.10 +... diff --git a/workflow/envs/ucsc-bedgraphtobigwig.yaml b/workflow/envs/ucsc-bedgraphtobigwig.yaml index 7b79a3a..f5af502 100644 --- a/workflow/envs/ucsc-bedgraphtobigwig.yaml +++ b/workflow/envs/ucsc-bedgraphtobigwig.yaml @@ -3,5 +3,5 @@ channels: - conda-forge - bioconda dependencies: - - ucsc-bedgraphtobigwig=377 + - ucsc-bedgraphtobigwig=455 ... diff --git a/workflow/envs/zgtf.yaml b/workflow/envs/zgtf.yaml index 9e71d51..577781c 100644 --- a/workflow/envs/zgtf.yaml +++ b/workflow/envs/zgtf.yaml @@ -3,5 +3,5 @@ channels: - conda-forge - bioconda dependencies: - - zgtf=0.1.1 + - zgtf=0.1.2 ... diff --git a/workflow/rules/htsinfer.smk b/workflow/rules/htsinfer.smk index c67e299..11cf6f2 100644 --- a/workflow/rules/htsinfer.smk +++ b/workflow/rules/htsinfer.smk @@ -49,7 +49,7 @@ rule run_htsinfer: cluster_log_path=CLUSTER_LOG, threads: 4 singularity: - "docker://zavolab/htsinfer:latest" + "docker://quay.io/biocontainers/htsinfer:0.9.0--pyhdfd78af_0" conda: os.path.join(workflow.basedir, "..", "envs", "htsinfer.yaml") log: @@ -82,7 +82,7 @@ rule htsinfer_to_tsv: SAMPLES_OUT, threads: 4 singularity: - "docker://zavolab/htsinfer:latest" + "docker://quay.io/biocontainers/htsinfer:0.9.0--pyhdfd78af_0" conda: os.path.join(workflow.basedir, "..", "envs", "htsinfer.yaml") log: diff --git a/workflow/rules/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk index 2521c49..437cbcf 100644 --- a/workflow/rules/paired_end.snakefile.smk +++ b/workflow/rules/paired_end.snakefile.smk @@ -64,7 +64,7 @@ rule pe_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 @@ -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 @@ -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 @@ -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 @@ -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:0.50.1--hc877fd6_0" conda: os.path.join(workflow.basedir, "envs", "kallisto.yaml") threads: 8 diff --git a/workflow/rules/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk index 0f25f6c..85c46f7 100644 --- a/workflow/rules/single_end.snakefile.smk +++ b/workflow/rules/single_end.snakefile.smk @@ -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 @@ -112,7 +112,7 @@ rule 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 @@ -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 @@ -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 @@ -409,7 +409,7 @@ rule genome_quantification_kallisto: ), ), container: - "docker://quay.io/biocontainers/kallisto:0.46.2--h60f4f9f_2" + "docker://quay.io/biocontainers/kallisto:0.50.1--hc877fd6_0" conda: os.path.join(workflow.basedir, "envs", "kallisto.yaml") threads: 8 diff --git a/workflow/rules/sra_download.smk b/workflow/rules/sra_download.smk index f4f73da..485a484 100644 --- a/workflow/rules/sra_download.smk +++ b/workflow/rules/sra_download.smk @@ -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" @@ -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" @@ -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" From 12f7c9b9980fb5c70d897de45022f94cbc2593bc Mon Sep 17 00:00:00 2001 From: Alex Kanitz Date: Fri, 2 Feb 2024 10:29:46 +0100 Subject: [PATCH 2/8] upgrade HTSinfer to 0.10.0 --- workflow/envs/htsinfer.yaml | 2 +- workflow/rules/htsinfer.smk | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/workflow/envs/htsinfer.yaml b/workflow/envs/htsinfer.yaml index 1a956d0..c25f872 100644 --- a/workflow/envs/htsinfer.yaml +++ b/workflow/envs/htsinfer.yaml @@ -2,5 +2,5 @@ channels: - bioconda dependencies: - - htsinfer=0.9.0 + - htsinfer=0.10.0 ... diff --git a/workflow/rules/htsinfer.smk b/workflow/rules/htsinfer.smk index 11cf6f2..450f16c 100644 --- a/workflow/rules/htsinfer.smk +++ b/workflow/rules/htsinfer.smk @@ -49,7 +49,7 @@ rule run_htsinfer: cluster_log_path=CLUSTER_LOG, threads: 4 singularity: - "docker://quay.io/biocontainers/htsinfer:0.9.0--pyhdfd78af_0" + "docker://quay.io/biocontainers/htsinfer:0.10.0--pyhdfd78af_0" conda: os.path.join(workflow.basedir, "..", "envs", "htsinfer.yaml") log: @@ -82,7 +82,7 @@ rule htsinfer_to_tsv: SAMPLES_OUT, threads: 4 singularity: - "docker://quay.io/biocontainers/htsinfer:0.9.0--pyhdfd78af_0" + "docker://quay.io/biocontainers/htsinfer:0.10.0--pyhdfd78af_0" conda: os.path.join(workflow.basedir, "..", "envs", "htsinfer.yaml") log: From 25031d5867a64ebc1d7b38e382c49008fa6e79d5 Mon Sep 17 00:00:00 2001 From: Alex Kanitz Date: Fri, 2 Feb 2024 12:14:27 +0100 Subject: [PATCH 3/8] downgrade kallisto back to 0.46.2 --- workflow/Snakefile | 2 +- workflow/envs/kallisto.yaml | 2 +- workflow/rules/paired_end.snakefile.smk | 2 +- workflow/rules/single_end.snakefile.smk | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/workflow/Snakefile b/workflow/Snakefile index d75ad90..078241b 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -612,7 +612,7 @@ rule create_index_kallisto: rule_config, current_rule=current_rule, immutable=("-i",) ), container: - "docker://quay.io/biocontainers/kallisto:0.50.1--hc877fd6_0" + "docker://quay.io/biocontainers/kallisto:0.46.2--h60f4f9f_2" conda: os.path.join(workflow.basedir, "envs", "kallisto.yaml") resources: diff --git a/workflow/envs/kallisto.yaml b/workflow/envs/kallisto.yaml index f928bb2..977d1cd 100644 --- a/workflow/envs/kallisto.yaml +++ b/workflow/envs/kallisto.yaml @@ -3,5 +3,5 @@ channels: - conda-forge - bioconda dependencies: - - kallisto=0.50.1 + - kallisto=0.46.2 ... diff --git a/workflow/rules/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk index 437cbcf..1aa3987 100644 --- a/workflow/rules/paired_end.snakefile.smk +++ b/workflow/rules/paired_end.snakefile.smk @@ -464,7 +464,7 @@ rule pe_genome_quantification_kallisto: ), ), container: - "docker://quay.io/biocontainers/kallisto:0.50.1--hc877fd6_0" + "docker://quay.io/biocontainers/kallisto:0.46.2--h60f4f9f_2" conda: os.path.join(workflow.basedir, "envs", "kallisto.yaml") threads: 8 diff --git a/workflow/rules/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk index 85c46f7..e45383f 100644 --- a/workflow/rules/single_end.snakefile.smk +++ b/workflow/rules/single_end.snakefile.smk @@ -409,7 +409,7 @@ rule genome_quantification_kallisto: ), ), container: - "docker://quay.io/biocontainers/kallisto:0.50.1--hc877fd6_0" + "docker://quay.io/biocontainers/kallisto:0.46.2--h60f4f9f_2" conda: os.path.join(workflow.basedir, "envs", "kallisto.yaml") threads: 8 From 59b26850964d77e87cf20dabec43edba51244ef5 Mon Sep 17 00:00:00 2001 From: Alex Kanitz Date: Fri, 2 Feb 2024 20:29:00 +0100 Subject: [PATCH 4/8] bump kallisto to 0.48.0 --- workflow/Snakefile | 2 +- workflow/envs/kallisto.yaml | 2 +- workflow/rules/paired_end.snakefile.smk | 2 +- workflow/rules/single_end.snakefile.smk | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/workflow/Snakefile b/workflow/Snakefile index 078241b..bd5beff 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -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: diff --git a/workflow/envs/kallisto.yaml b/workflow/envs/kallisto.yaml index 977d1cd..07451b9 100644 --- a/workflow/envs/kallisto.yaml +++ b/workflow/envs/kallisto.yaml @@ -3,5 +3,5 @@ channels: - conda-forge - bioconda dependencies: - - kallisto=0.46.2 + - kallisto=0.48.0 ... diff --git a/workflow/rules/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk index 1aa3987..06e2b49 100644 --- a/workflow/rules/paired_end.snakefile.smk +++ b/workflow/rules/paired_end.snakefile.smk @@ -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 diff --git a/workflow/rules/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk index e45383f..d361ca5 100644 --- a/workflow/rules/single_end.snakefile.smk +++ b/workflow/rules/single_end.snakefile.smk @@ -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 From f20d98224dfd7549e6a1061b79071759b83a0225 Mon Sep 17 00:00:00 2001 From: Alex Kanitz Date: Fri, 2 Feb 2024 20:40:21 +0100 Subject: [PATCH 5/8] roll back source for htsinfer image --- workflow/rules/htsinfer.smk | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflow/rules/htsinfer.smk b/workflow/rules/htsinfer.smk index 450f16c..c67e299 100644 --- a/workflow/rules/htsinfer.smk +++ b/workflow/rules/htsinfer.smk @@ -49,7 +49,7 @@ rule run_htsinfer: cluster_log_path=CLUSTER_LOG, threads: 4 singularity: - "docker://quay.io/biocontainers/htsinfer:0.10.0--pyhdfd78af_0" + "docker://zavolab/htsinfer:latest" conda: os.path.join(workflow.basedir, "..", "envs", "htsinfer.yaml") log: @@ -82,7 +82,7 @@ rule htsinfer_to_tsv: SAMPLES_OUT, threads: 4 singularity: - "docker://quay.io/biocontainers/htsinfer:0.10.0--pyhdfd78af_0" + "docker://zavolab/htsinfer:latest" conda: os.path.join(workflow.basedir, "..", "envs", "htsinfer.yaml") log: From 7efba8f07f0a7333cd756b885b97eb2424195424 Mon Sep 17 00:00:00 2001 From: Alex Kanitz Date: Fri, 2 Feb 2024 21:58:26 +0100 Subject: [PATCH 6/8] update MD5 sums --- .../expected_output.md5 | 114 +++++++++--------- 1 file changed, 57 insertions(+), 57 deletions(-) diff --git a/tests/test_integration_workflow_with_conda/expected_output.md5 b/tests/test_integration_workflow_with_conda/expected_output.md5 index 338761a..321bd17 100644 --- a/tests/test_integration_workflow_with_conda/expected_output.md5 +++ b/tests/test_integration_workflow_with_conda/expected_output.md5 @@ -1,5 +1,5 @@ cbaebdb67aee4784b64aff7fec9fda42 results/kallisto_indexes/homo_sapiens/kallisto.idx -204865f645102587c4953fccb256797c results/salmon_indexes/homo_sapiens/31/salmon.idx/versionInfo.json +f06db51ed32dec928fe518075deb4f2e results/salmon_indexes/homo_sapiens/31/salmon.idx/versionInfo.json 51b5292e3a874119c0e1aa566e95d70c results/salmon_indexes/homo_sapiens/31/salmon.idx/duplicate_clusters.tsv 4e10114bb8f9096d594776181424a302 results/salmon_indexes/homo_sapiens/31/salmon.idx/info.json dee7cdc194d5d0617552b7a3b5ad8dfb results/star_indexes/homo_sapiens/75/STAR_index/chrLength.txt @@ -20,45 +20,45 @@ ea36f062eedc7f54ceffea2b635a25a8 results/star_indexes/homo_sapiens/75/STAR_inde 500dd49da40b16799aba62aa5cf239ba results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1.pe.remove_polya.fastq e90e31db1ce51d930645eb74ff70d21b results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_adapters.fastq 1c0796d7e0bdab0e99780b2e11d80c19 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya.fastq -9896744dd90ff3eef00c91fa1f721366 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results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/per_sequence_gc_content.png +c1c267daf0b12f68d9b565a7deb123cf results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/per_sequence_quality.png f399fa5792cdfb72fac7ae2226723122 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/per_tile_quality.png -3634e72357f77330f23ba4959279f362 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/sequence_length_distribution.png +3ebe15878142b0967f366956e5e6120d results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/sequence_length_distribution.png From 913385e77c1564a77885745a7c1a8d4cf20c7131 Mon Sep 17 00:00:00 2001 From: Alex Kanitz Date: Fri, 2 Feb 2024 22:12:40 +0100 Subject: [PATCH 7/8] update MD5 sums --- .../expected_output.md5 | 114 +++++++++--------- .../expected_output.md5 | 114 +++++++++--------- 2 files changed, 114 insertions(+), 114 deletions(-) diff --git a/tests/test_integration_workflow/expected_output.md5 b/tests/test_integration_workflow/expected_output.md5 index 338761a..321bd17 100644 --- a/tests/test_integration_workflow/expected_output.md5 +++ b/tests/test_integration_workflow/expected_output.md5 @@ -1,5 +1,5 @@ cbaebdb67aee4784b64aff7fec9fda42 results/kallisto_indexes/homo_sapiens/kallisto.idx -204865f645102587c4953fccb256797c results/salmon_indexes/homo_sapiens/31/salmon.idx/versionInfo.json 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results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/per_base_sequence_content.png +2a12a72a2e561b61d2629ddee40e7ca4 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/per_sequence_gc_content.png +c1c267daf0b12f68d9b565a7deb123cf results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/per_sequence_quality.png f399fa5792cdfb72fac7ae2226723122 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/per_tile_quality.png -3634e72357f77330f23ba4959279f362 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/sequence_length_distribution.png +3ebe15878142b0967f366956e5e6120d results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/sequence_length_distribution.png From 6924b179f7c5b118de09ab8acaf53742c8c895f6 Mon Sep 17 00:00:00 2001 From: Alex Kanitz Date: Sat, 3 Feb 2024 18:24:55 +0100 Subject: [PATCH 8/8] update MD5 sums; all test scripts executable --- tests/test_format/test_snakefmt.sh | 0 tests/test_format/test_snakemake_lint.sh | 0 .../expected_output.md5 | 84 ++++++------ .../expected_output_temp_flag.md5 | 122 ++++++++---------- .../expected_output.md5 | 84 ++++++------ .../test.local.sh | 0 .../test.slurm.sh | 0 7 files changed, 141 insertions(+), 149 deletions(-) mode change 100644 => 100755 tests/test_format/test_snakefmt.sh mode change 100644 => 100755 tests/test_format/test_snakemake_lint.sh mode change 100644 => 100755 tests/test_sra_download_with_conda/test.local.sh mode change 100644 => 100755 tests/test_sra_download_with_conda/test.slurm.sh diff --git a/tests/test_format/test_snakefmt.sh b/tests/test_format/test_snakefmt.sh old mode 100644 new mode 100755 diff --git a/tests/test_format/test_snakemake_lint.sh b/tests/test_format/test_snakemake_lint.sh old mode 100644 new mode 100755 diff --git a/tests/test_integration_workflow/expected_output.md5 b/tests/test_integration_workflow/expected_output.md5 index 321bd17..d7749ca 100644 --- a/tests/test_integration_workflow/expected_output.md5 +++ b/tests/test_integration_workflow/expected_output.md5 @@ -26,39 +26,39 @@ e90e31db1ce51d930645eb74ff70d21b results/samples/synthetic_10_reads_paired_synt 2dfb54adde8d7c9c0d6e4985b9346f4a 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