diff --git a/bio/seqkit/fx2tab/environment.yaml b/bio/seqkit/environment.yaml similarity index 100% rename from bio/seqkit/fx2tab/environment.yaml rename to bio/seqkit/environment.yaml diff --git a/bio/seqkit/fx2tab/meta.yaml b/bio/seqkit/fx2tab/meta.yaml deleted file mode 100644 index 424b432fa9..0000000000 --- a/bio/seqkit/fx2tab/meta.yaml +++ /dev/null @@ -1,14 +0,0 @@ -name: SeqKit fx2tab -url: https://bioinf.shenwei.me/seqkit/usage/#fx2tab -description: | - Run SeqKit f2tab convert FASTA/Q to tabular format. -authors: - - Filipe G. Vieira -input: - - fastx: Input FASTA/Q file -output: - - tsv: Output TSV file -params: - - extra: Optional parameters -notes: | - * The `extra` param allows for additional program arguments. diff --git a/bio/seqkit/fx2tab/test/Snakefile b/bio/seqkit/fx2tab/test/Snakefile deleted file mode 100644 index 12baa73adc..0000000000 --- a/bio/seqkit/fx2tab/test/Snakefile +++ /dev/null @@ -1,12 +0,0 @@ -rule seqkit_fx2tab: - input: - fastx="reads/{sample}.fastq", - output: - tsv="out/fx2tab/{sample}.tsv", - log: - "logs/fx2tab/{sample}.log", - params: - extra="--name", - threads: 2 - wrapper: - "master/bio/seqkit/fx2tab" diff --git a/bio/seqkit/fx2tab/test/reads/a.fastq b/bio/seqkit/fx2tab/test/reads/a.fastq deleted file mode 100644 index 7852992494..0000000000 --- a/bio/seqkit/fx2tab/test/reads/a.fastq +++ /dev/null @@ -1,8 +0,0 @@ -@1 -ACGGCAT -+ -!!!!!!! -@2 -ATGGCAT -+ -!!!!!!! diff --git a/bio/seqkit/fx2tab/wrapper.py b/bio/seqkit/fx2tab/wrapper.py deleted file mode 100644 index ac17f9c76b..0000000000 --- a/bio/seqkit/fx2tab/wrapper.py +++ /dev/null @@ -1,18 +0,0 @@ -__author__ = "Filipe G. Vieira" -__copyright__ = "Copyright 2023, Filipe G. Vieira" -__license__ = "MIT" - -from snakemake.shell import shell - -extra = snakemake.params.get("extra", "") -log = snakemake.log_fmt_shell(stdout=True, stderr=True) - - -shell( - "seqkit fx2tab" - " --threads {snakemake.threads}" - " {extra}" - " --out-file {snakemake.output.tsv}" - " {snakemake.input.fastx}" - " {log}" -) diff --git a/bio/seqkit/grep/environment.yaml b/bio/seqkit/grep/environment.yaml deleted file mode 100644 index 4db3bf6dd6..0000000000 --- a/bio/seqkit/grep/environment.yaml +++ /dev/null @@ -1,6 +0,0 @@ -channels: - - conda-forge - - bioconda - - nodefaults -dependencies: - - seqkit =2.4.0 diff --git a/bio/seqkit/grep/meta.yaml b/bio/seqkit/grep/meta.yaml deleted file mode 100644 index e75b3bed7b..0000000000 --- a/bio/seqkit/grep/meta.yaml +++ /dev/null @@ -1,15 +0,0 @@ -name: SeqKit grep -url: https://bioinf.shenwei.me/seqkit/usage/#grep -description: | - Run SeqKit grep to search sequences by ID, name, sequence, or sequence motifs. -authors: - - Filipe G. Vieira -input: - - fastx: Input FASTA/Q file - - pattern: pattern file (one record per line) -output: - - fastx: Output FASTA/Q file -params: - - extra: Optional parameters -notes: | - * The `extra` param allows for additional program arguments. diff --git a/bio/seqkit/grep/test/Snakefile b/bio/seqkit/grep/test/Snakefile deleted file mode 100644 index 1bde038c70..0000000000 --- a/bio/seqkit/grep/test/Snakefile +++ /dev/null @@ -1,28 +0,0 @@ -rule seqkit_grep_name: - input: - fastx="reads/{sample}.fastq", - patterns="reads/name.txt", - output: - fastx="out/grep_name/{sample}.fastq.gz", - log: - "logs/grep_name/{sample}.log", - params: - extra="--by-name", - threads: 2 - wrapper: - "master/bio/seqkit/grep" - - -rule seqkit_grep_seq: - input: - fastx="reads/{sample}.fastq", - patterns="reads/seq.txt", - output: - fastx="out/grep_seq/{sample}.fastq.gz", - log: - "logs/grep_seq/{sample}.log", - params: - extra="--by-seq", - threads: 2 - wrapper: - "master/bio/seqkit/grep" diff --git a/bio/seqkit/grep/test/reads/a.fastq b/bio/seqkit/grep/test/reads/a.fastq deleted file mode 100644 index 7852992494..0000000000 --- a/bio/seqkit/grep/test/reads/a.fastq +++ /dev/null @@ -1,8 +0,0 @@ -@1 -ACGGCAT -+ -!!!!!!! -@2 -ATGGCAT -+ -!!!!!!! diff --git a/bio/seqkit/grep/wrapper.py b/bio/seqkit/grep/wrapper.py deleted file mode 100644 index 1e69866467..0000000000 --- a/bio/seqkit/grep/wrapper.py +++ /dev/null @@ -1,19 +0,0 @@ -__author__ = "Filipe G. Vieira" -__copyright__ = "Copyright 2023, Filipe G. Vieira" -__license__ = "MIT" - -from snakemake.shell import shell - -extra = snakemake.params.get("extra", "") -log = snakemake.log_fmt_shell(stdout=True, stderr=True) - - -shell( - "seqkit grep" - " --threads {snakemake.threads}" - " --pattern-file {snakemake.input.patterns}" - " {extra}" - " --out-file {snakemake.output.fastx}" - " {snakemake.input.fastx}" - " {log}" -) diff --git a/bio/seqkit/meta.yaml b/bio/seqkit/meta.yaml new file mode 100644 index 0000000000..0343ec2a07 --- /dev/null +++ b/bio/seqkit/meta.yaml @@ -0,0 +1,16 @@ +name: SeqKit generic wrapper +url: https://bioinf.shenwei.me/seqkit/usage/ +description: | + Run SeqKit. +authors: + - Filipe G. Vieira +input: + - input file(s) +output: + - output file(s) +params: + - command: SeqKit command to use. + - extra: Optional parameters. +notes: | + * First `input` and `output` file is considered to be the main one. + * Keys for extra `input` and `output` files need to match `seqkit` arguments without the `-file` suffix (if present). diff --git a/bio/seqkit/rmdup/environment.yaml b/bio/seqkit/rmdup/environment.yaml deleted file mode 100644 index 4db3bf6dd6..0000000000 --- a/bio/seqkit/rmdup/environment.yaml +++ /dev/null @@ -1,6 +0,0 @@ -channels: - - conda-forge - - bioconda - - nodefaults -dependencies: - - seqkit =2.4.0 diff --git a/bio/seqkit/rmdup/meta.yaml b/bio/seqkit/rmdup/meta.yaml deleted file mode 100644 index f2a601c62b..0000000000 --- a/bio/seqkit/rmdup/meta.yaml +++ /dev/null @@ -1,16 +0,0 @@ -name: SeqKit rmdup -url: https://bioinf.shenwei.me/seqkit/usage/#rmdup -description: | - Run SeqKit rmdup grep to remove duplicated sequences by ID, name, or sequence. -authors: - - Filipe G. Vieira -input: - - fastx: Input FASTA/Q file -output: - - fastx: Output FASTA/Q file - - dup_num: Output file to save number and list of duplicated seqs - - dup_seq: Output file to save duplicated seqs -params: - - extra: Optional parameters -notes: | - * The `extra` param allows for additional program arguments. diff --git a/bio/seqkit/rmdup/test/Snakefile b/bio/seqkit/rmdup/test/Snakefile deleted file mode 100644 index b3fa86af1b..0000000000 --- a/bio/seqkit/rmdup/test/Snakefile +++ /dev/null @@ -1,30 +0,0 @@ -rule seqkit_rmdup_name: - input: - fastx="reads/{sample}.fastq", - output: - fastx="out/rmdup_name/{sample}.fastq.gz", - dup_num="out/rmdup_name/{sample}.num.txt", - dup_seq="out/rmdup_name/{sample}.seq.txt", - log: - "logs/rmdup_name/{sample}.log", - params: - extra="--by-name", - threads: 2 - wrapper: - "master/bio/seqkit/rmdup" - - -rule seqkit_rmdup_seq: - input: - fastx="reads/{sample}.fastq", - output: - fastx="out/rmdup_seq/{sample}.fastq.gz", - dup_num="out/rmdup_seq/{sample}.num.txt", - dup_seq="out/rmdup_seq/{sample}.seq.txt", - log: - "logs/rmdup_seq/{sample}.log", - params: - extra="--by-seq", - threads: 2 - wrapper: - "master/bio/seqkit/rmdup" diff --git a/bio/seqkit/rmdup/wrapper.py b/bio/seqkit/rmdup/wrapper.py deleted file mode 100644 index 86f577304e..0000000000 --- a/bio/seqkit/rmdup/wrapper.py +++ /dev/null @@ -1,30 +0,0 @@ -__author__ = "Filipe G. Vieira" -__copyright__ = "Copyright 2023, Filipe G. Vieira" -__license__ = "MIT" - -from snakemake.shell import shell - -extra = snakemake.params.get("extra", "") -log = snakemake.log_fmt_shell(stdout=True, stderr=True) - - -dup_num = snakemake.output.get("dup_num", "") -if dup_num: - dup_num = f"--dup-num-file {dup_num}" - - -dup_seq = snakemake.output.get("dup_seq", "") -if dup_seq: - dup_seq = f"--dup-seqs-file {dup_seq}" - - -shell( - "seqkit rmdup" - " --threads {snakemake.threads}" - " {extra}" - " --out-file {snakemake.output.fastx}" - " {dup_num}" - " {dup_seq}" - " {snakemake.input.fastx}" - " {log}" -) diff --git a/bio/seqkit/stats/environment.yaml b/bio/seqkit/stats/environment.yaml deleted file mode 100644 index 4db3bf6dd6..0000000000 --- a/bio/seqkit/stats/environment.yaml +++ /dev/null @@ -1,6 +0,0 @@ -channels: - - conda-forge - - bioconda - - nodefaults -dependencies: - - seqkit =2.4.0 diff --git a/bio/seqkit/stats/meta.yaml b/bio/seqkit/stats/meta.yaml deleted file mode 100644 index 25e43f2ca2..0000000000 --- a/bio/seqkit/stats/meta.yaml +++ /dev/null @@ -1,14 +0,0 @@ -name: SeqKit stats -url: https://bioinf.shenwei.me/seqkit/usage/#stats -description: | - Run SeqKit stats to get simple statistics of FASTA/Q files. -authors: - - Filipe G. Vieira -input: - - fastx: Input FASTA/Q file -output: - - stats: Output stats file -params: - - extra: Optional parameters -notes: | - * The `extra` param allows for additional program arguments. diff --git a/bio/seqkit/stats/test/Snakefile b/bio/seqkit/stats/test/Snakefile deleted file mode 100644 index 4b143600eb..0000000000 --- a/bio/seqkit/stats/test/Snakefile +++ /dev/null @@ -1,12 +0,0 @@ -rule seqkit_stats: - input: - fastx="reads/{sample}.fastq", - output: - stats="out/stats/{sample}.tsv", - log: - "logs/stats/{sample}.log", - params: - extra="--all --tabular", - threads: 2 - wrapper: - "master/bio/seqkit/stats" diff --git a/bio/seqkit/stats/test/reads/a.fastq b/bio/seqkit/stats/test/reads/a.fastq deleted file mode 100644 index 7852992494..0000000000 --- a/bio/seqkit/stats/test/reads/a.fastq +++ /dev/null @@ -1,8 +0,0 @@ -@1 -ACGGCAT -+ -!!!!!!! -@2 -ATGGCAT -+ -!!!!!!! diff --git a/bio/seqkit/stats/wrapper.py b/bio/seqkit/stats/wrapper.py deleted file mode 100644 index 5c1354a814..0000000000 --- a/bio/seqkit/stats/wrapper.py +++ /dev/null @@ -1,18 +0,0 @@ -__author__ = "Filipe G. Vieira" -__copyright__ = "Copyright 2023, Filipe G. Vieira" -__license__ = "MIT" - -from snakemake.shell import shell - -extra = snakemake.params.get("extra", "") -log = snakemake.log_fmt_shell(stdout=True, stderr=True) - - -shell( - "seqkit stats" - " --threads {snakemake.threads}" - " {extra}" - " --out-file {snakemake.output.stats}" - " {snakemake.input.fastx}" - " {log}" -) diff --git a/bio/seqkit/subseq/environment.yaml b/bio/seqkit/subseq/environment.yaml deleted file mode 100644 index 4db3bf6dd6..0000000000 --- a/bio/seqkit/subseq/environment.yaml +++ /dev/null @@ -1,6 +0,0 @@ -channels: - - conda-forge - - bioconda - - nodefaults -dependencies: - - seqkit =2.4.0 diff --git a/bio/seqkit/subseq/meta.yaml b/bio/seqkit/subseq/meta.yaml deleted file mode 100644 index d8f34416a2..0000000000 --- a/bio/seqkit/subseq/meta.yaml +++ /dev/null @@ -1,13 +0,0 @@ -name: SeqKit subseq -url: https://bioinf.shenwei.me/seqkit/usage/#subseq -description: | - Run SeqKit grep to get subsequences by region/gtf/bed, including flanking sequences. -authors: - - Connor McEntee -input: - - fasta: Input FASTA file - - gtf: GTF (version 2.2) file -output: - - fasta: Output FASTA file -params: - - extra: Optional parameters diff --git a/bio/seqkit/subseq/test/Snakefile b/bio/seqkit/subseq/test/Snakefile deleted file mode 100644 index fd1d390392..0000000000 --- a/bio/seqkit/subseq/test/Snakefile +++ /dev/null @@ -1,40 +0,0 @@ -rule seqkit_subseq_bed: - input: - fasta="sequences/t.fa", - bed="sequences/t.bed", - output: - fasta="out/subseq_bed/t_bed.fa.gz", - log: - "logs/subseq_bed/bed.log", - threads: 2 - wrapper: - "master/bio/seqkit/subseq" - - -rule seqkit_subseq_gtf: - input: - fasta="sequences/t.fa", - gtf="sequences/t.gtf", - output: - fasta="out/subseq_gtf/t_gtf.fa.gz", - log: - "logs/subseq_gtf/gtf.log", - params: - extra="--feature CDS", - threads: 2 - wrapper: - "master/bio/seqkit/subseq" - - -rule seqkit_subseq_region: - input: - fasta="sequences/t.fa", - output: - fasta="out/subseq_region/t_region.fa.gz", - log: - "logs/subseq_region/region.log", - params: - extra="--region 1:12", - threads: 2 - wrapper: - "master/bio/seqkit/subseq" diff --git a/bio/seqkit/subseq/test/sequences/t.fa b/bio/seqkit/subseq/test/sequences/t.fa deleted file mode 100644 index 63d1d12c45..0000000000 --- a/bio/seqkit/subseq/test/sequences/t.fa +++ /dev/null @@ -1,3 +0,0 @@ ->seq -actgACTGactgn - diff --git a/bio/seqkit/subseq/wrapper.py b/bio/seqkit/subseq/wrapper.py deleted file mode 100644 index a7914de702..0000000000 --- a/bio/seqkit/subseq/wrapper.py +++ /dev/null @@ -1,27 +0,0 @@ -__author__ = "Connor McEntee" -__license__ = "MIT" - -from snakemake.shell import shell - -extra = snakemake.params.get("extra", "") -log = snakemake.log_fmt_shell(stdout=True, stderr=True) - -bed = snakemake.input.get("bed", "") -if bed: - bed = f"--bed {bed}" - -gtf = snakemake.input.get("gtf", "") -if gtf: - gtf = f"--gtf {gtf}" - - -shell( - "seqkit subseq" - " --threads {snakemake.threads}" - " {bed}" - " {gtf}" - " {extra}" - " --out-file {snakemake.output.fasta}" - " {snakemake.input.fasta}" - " {log}" -) diff --git a/bio/seqkit/test/Snakefile b/bio/seqkit/test/Snakefile new file mode 100644 index 0000000000..6e41279596 --- /dev/null +++ b/bio/seqkit/test/Snakefile @@ -0,0 +1,155 @@ +rule seqkit_seq: + input: + fasta="data/{sample}.fa", + output: + fasta="out/seq/{sample}.fa.gz", + log: + "logs/seq/{sample}.log", + params: + command="seq", + extra="--min-len 10", + threads: 2 + wrapper: + "master/bio/seqkit" + + +rule seqkit_subseq_bed: + input: + fasta="data/{sample}.fa", + bed="data/{sample}.bed", + output: + fasta="out/subseq/bed/{sample}.fa.gz", + log: + "logs/subseq/bed/{sample}.log", + params: + command="subseq", + threads: 2 + wrapper: + "master/bio/seqkit" + + +rule seqkit_subseq_gtf: + input: + fasta="data/{sample}.fa", + gtf="data/{sample}.gtf", + output: + fasta="out/subseq/gtf/{sample}.fa.gz", + log: + "logs/subseq/gtf/{sample}.log", + params: + command="subseq", + extra="--feature CDS", + threads: 2 + wrapper: + "master/bio/seqkit" + + +rule seqkit_subseq_region: + input: + fasta="data/{sample}.fa", + output: + fasta="out/subseq/region/{sample}.fa.gz", + log: + "logs/subseq/region/{sample}.log", + params: + command="subseq", + extra="--region 1:12", + threads: 2 + wrapper: + "master/bio/seqkit" + + +rule seqkit_fx2tab: + input: + fastx="data/{sample}.fastq", + output: + tsv="out/fx2tab/{sample}.tsv", + log: + "logs/fx2tab/{sample}.log", + params: + command="fx2tab", + extra="--name", + threads: 2 + wrapper: + "master/bio/seqkit" + + +rule seqkit_grep_name: + input: + fastx="data/{sample}.fastq", + pattern="data/name.txt", + output: + fastx="out/grep/name/{sample}.fastq.gz", + log: + "logs/grep/name/{sample}.log", + params: + command="grep", + extra="--by-name", + threads: 2 + wrapper: + "master/bio/seqkit" + + +rule seqkit_grep_seq: + input: + fastx="data/{sample}.fastq", + pattern="data/seq.txt", + output: + fastx="out/grep/seq/{sample}.fastq.gz", + log: + "logs/grep/seq/{sample}.log", + params: + command="grep", + extra="--by-seq", + threads: 2 + wrapper: + "master/bio/seqkit" + + +rule seqkit_rmdup_name: + input: + fastx="data/{sample}.fastq", + output: + fastx="out/rmdup/name/{sample}.fastq.gz", + dup_num="out/rmdup/name/{sample}.num.txt", + dup_seqs="out/rmdup/name/{sample}.seq.txt", + log: + "logs/rmdup/name/{sample}.log", + params: + command="rmdup", + extra="--by-name", + threads: 2 + wrapper: + "master/bio/seqkit" + + +rule seqkit_rmdup_seq: + input: + fastx="data/{sample}.fastq", + output: + fastx="out/rmdup/seq/{sample}.fastq.gz", + dup_num="out/rmdup/seq/{sample}.num.txt", + dup_seqs="out/rmdup/seq/{sample}.seq.txt", + log: + "logs/rmdup/seq/{sample}.log", + params: + command="rmdup", + extra="--by-seq", + threads: 2 + wrapper: + "master/bio/seqkit" + + +rule seqkit_stats: + input: + fastx="data/{sample}.fastq", + output: + stats="out/stats/{sample}.tsv", + log: + "logs/stats/{sample}.log", + params: + command="stats", + extra="--all --tabular", + threads: 2 + wrapper: + "master/bio/seqkit" diff --git a/bio/seqkit/subseq/test/sequences/t.bed b/bio/seqkit/test/data/a.bed similarity index 100% rename from bio/seqkit/subseq/test/sequences/t.bed rename to bio/seqkit/test/data/a.bed diff --git a/bio/seqkit/test/data/a.fa b/bio/seqkit/test/data/a.fa new file mode 100644 index 0000000000..c28e23fbe8 --- /dev/null +++ b/bio/seqkit/test/data/a.fa @@ -0,0 +1,4 @@ +>seq1 +actgACTGactgn +>seq2 +actg diff --git a/bio/seqkit/rmdup/test/reads/a.fastq b/bio/seqkit/test/data/a.fastq similarity index 100% rename from bio/seqkit/rmdup/test/reads/a.fastq rename to bio/seqkit/test/data/a.fastq diff --git a/bio/seqkit/subseq/test/sequences/t.gtf b/bio/seqkit/test/data/a.gtf similarity index 100% rename from bio/seqkit/subseq/test/sequences/t.gtf rename to bio/seqkit/test/data/a.gtf diff --git a/bio/seqkit/grep/test/reads/name.txt b/bio/seqkit/test/data/name.txt similarity index 100% rename from bio/seqkit/grep/test/reads/name.txt rename to bio/seqkit/test/data/name.txt diff --git a/bio/seqkit/grep/test/reads/seq.txt b/bio/seqkit/test/data/seq.txt similarity index 100% rename from bio/seqkit/grep/test/reads/seq.txt rename to bio/seqkit/test/data/seq.txt diff --git a/bio/seqkit/wrapper.py b/bio/seqkit/wrapper.py new file mode 100644 index 0000000000..9833cb1af8 --- /dev/null +++ b/bio/seqkit/wrapper.py @@ -0,0 +1,40 @@ +__author__ = "Filipe G. Vieira" +__copyright__ = "Copyright 2023, Filipe G. Vieira" +__license__ = "MIT" + +from snakemake.shell import shell + + +extra = snakemake.params.get("extra", "") +log = snakemake.log_fmt_shell(stdout=True, stderr=True) + + +extra_input = " ".join( + [ + f"--{key.replace('_','-')} {value}" + if key in ["bed", "gtf"] + else f"--{key.replace('_','-')}-file {value}" + for key, value in snakemake.input.items() + ][1:] +) + +extra_output = " ".join( + [ + f"--{key.replace('_','-')} {value}" + if key in ["read1", "read2"] + else f"--{key.replace('_','-')}-file {value}" + for key, value in snakemake.output.items() + ][1:] +) + + +shell( + "seqkit {snakemake.params.command}" + " --threads {snakemake.threads}" + " {extra_input}" + " {extra_output}" + " {extra}" + " --out-file {snakemake.output[0]}" + " {snakemake.input[0]}" + " {log}" +) diff --git a/test.py b/test.py index 02e3050480..7300eb3ecc 100644 --- a/test.py +++ b/test.py @@ -251,7 +251,7 @@ def test_tadpole(): @skip_if_not_modified def test_seqkit_stats(): run( - "bio/seqkit/stats", + "bio/seqkit", [ "snakemake", "--cores", @@ -266,25 +266,25 @@ def test_seqkit_stats(): @skip_if_not_modified def test_seqkit_rmdup(): run( - "bio/seqkit/rmdup", + "bio/seqkit", [ "snakemake", "--cores", "2", "--use-conda", "-F", - "out/rmdup_name/a.fastq.gz", + "out/rmdup/name/a.fastq.gz", ], ) run( - "bio/seqkit/rmdup", + "bio/seqkit", [ "snakemake", "--cores", "2", "--use-conda", "-F", - "out/rmdup_seq/a.fastq.gz", + "out/rmdup/seq/a.fastq.gz", ], ) @@ -300,7 +300,7 @@ def test_gffread(): @skip_if_not_modified def test_seqkit_fx2tab(): run( - "bio/seqkit/fx2tab", + "bio/seqkit", [ "snakemake", "--cores", @@ -315,25 +315,25 @@ def test_seqkit_fx2tab(): @skip_if_not_modified def test_seqkit_grep(): run( - "bio/seqkit/grep", + "bio/seqkit", [ "snakemake", "--cores", "2", "--use-conda", "-F", - "out/grep_name/a.fastq.gz", + "out/grep/name/a.fastq.gz", ], ) run( - "bio/seqkit/grep", + "bio/seqkit", [ "snakemake", "--cores", "2", "--use-conda", "-F", - "out/grep_seq/a.fastq.gz", + "out/grep/seq/a.fastq.gz", ], ) @@ -341,36 +341,51 @@ def test_seqkit_grep(): @skip_if_not_modified def test_seqkit_subseq(): run( - "bio/seqkit/subseq", + "bio/seqkit", [ "snakemake", "--cores", "2", "--use-conda", "-F", - "out/subseq_bed/t_bed.fa.gz", + "out/subseq/bed/a.fa.gz", ], ) run( - "bio/seqkit/subseq", + "bio/seqkit", [ "snakemake", "--cores", "2", "--use-conda", "-F", - "out/subseq_gtf/t_gtf.fa.gz", + "out/subseq/gtf/a.fa.gz", ], ) run( - "bio/seqkit/subseq", + "bio/seqkit", [ "snakemake", "--cores", "2", "--use-conda", "-F", - "out/subseq_region/t_region.fa.gz", + "out/subseq/region/a.fa.gz", + ], + ) + + +@skip_if_not_modified +def test_seqkit_seq(): + run( + "bio/seqkit", + [ + "snakemake", + "--cores", + "2", + "--use-conda", + "-F", + "out/seq/a.fa.gz", ], )