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nf-core_modules/tests/modules/blast/blastn/test.yml

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Adding blast blastn module
2021-02-09 10:58:36 -05:00
- name: blast_blastn
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 05:10:18 -04:00
command: nextflow run ./tests/modules/blast/blastn -entry test_blast_blastn -c tests/config/nextflow.config
Adding blast blastn module
2021-02-09 10:58:36 -05:00
tags:
- blast
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 04:10:52 -04:00
- blast/blastn
Adding blast blastn module
2021-02-09 10:58:36 -05:00
files:
Converge test data usage (#249) * initial data restructuing * fixed bedtools_complement * fixed bedtools_genomecov * fixed bedtools_getfasta * fixed bedtools_intersect * fixed bedtools maskfasta * fixed bedtools_merge * fixed bedtools_slop * fixed bedtools_sort * fixed bismark_genome_preparation * fixed blast * fixed bowtie data * fixed bowtie2 data * fixed bwa data * fixed bwamem2 data usage * fixed cat_fastq data * fixed cutadapt data * fixed dsh data * fixed fastp data * fixed fastqc; fixed bug with wrong fastq format * fixed gatk * fixed data for gffread, gunzip * fixed ivar paths * fixed data paths for minimap2 * fixed mosdepth * fixed multiqc, pangolin * fixed picard data paths * fixed data paths for qualimap, quast * fixed salmon data paths * fixed samtools paths * fixed seqwish, stringtie paths * fixed tabix, trimgalore paths * cleaned up data * added first description to README * changed test data naming again; everything up to bwa fixed * everything up to gatk4 * fixed everything up to ivar * fixed everything up to picard * everything up to quast * everything fixed up to stringtie * switched everyting to 'test' naming scheme * fixed samtools and ivar tests * cleaned up README a bit * add (simulated) methylation test data based on SARS-CoV-2 genome; simulated with Sherman --non_dir --genome sarscov2/fasta/ --paired -n 10000 -l 100 --CG 20 --CH 90 * bwameth/align: update data paths and checksums also, build index on the go * bwameth/index: update data paths and checksums * methyldackel/extract: update data paths and checksums * methyldackel/mbias: update data paths and checksums * bismark/deduplicate: update data paths and checksums * remove obsolete testdata * remove empty 'dummy_file.txt' * update data/README.md * methyldackel: fix test * Revert "methyldackel: fix test" This reverts commit f175a32d144b1b0bfa0c6885da80c51e3cfe038a. * methyldackel: fix test for real * move test.genome.sizes * changed test names * switched genomic to genome and transcriptome * fix bedtools, blast * fix gtf, tabix, .paf * fix bowtie,bwa,bwameth * fixed: bwa, bwamem, gatk, gffread, quast * fixed bismark and blast * fixed remaining tests * delete bam file Co-authored-by: phue <patrick.huether@gmail.com>
2021-03-04 05:10:57 -05:00
- path: ./output/blast/test.blastn.txt
update tests for new config (#384) * update tests for new config * fix quast, update more * more updates! * more tests updated * fix tests, added tabix gff3.gz * Delete main.nf Removing SPAdes from PR to avoid merge conflicts with https://github.com/nf-core/modules/pull/396 Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-01 15:22:06 -04:00
- path: ./output/blast/blast_db/genome.fasta.nsq
Converge test data usage (#249) * initial data restructuing * fixed bedtools_complement * fixed bedtools_genomecov * fixed bedtools_getfasta * fixed bedtools_intersect * fixed bedtools maskfasta * fixed bedtools_merge * fixed bedtools_slop * fixed bedtools_sort * fixed bismark_genome_preparation * fixed blast * fixed bowtie data * fixed bowtie2 data * fixed bwa data * fixed bwamem2 data usage * fixed cat_fastq data * fixed cutadapt data * fixed dsh data * fixed fastp data * fixed fastqc; fixed bug with wrong fastq format * fixed gatk * fixed data for gffread, gunzip * fixed ivar paths * fixed data paths for minimap2 * fixed mosdepth * fixed multiqc, pangolin * fixed picard data paths * fixed data paths for qualimap, quast * fixed salmon data paths * fixed samtools paths * fixed seqwish, stringtie paths * fixed tabix, trimgalore paths * cleaned up data * added first description to README * changed test data naming again; everything up to bwa fixed * everything up to gatk4 * fixed everything up to ivar * fixed everything up to picard * everything up to quast * everything fixed up to stringtie * switched everyting to 'test' naming scheme * fixed samtools and ivar tests * cleaned up README a bit * add (simulated) methylation test data based on SARS-CoV-2 genome; simulated with Sherman --non_dir --genome sarscov2/fasta/ --paired -n 10000 -l 100 --CG 20 --CH 90 * bwameth/align: update data paths and checksums also, build index on the go * bwameth/index: update data paths and checksums * methyldackel/extract: update data paths and checksums * methyldackel/mbias: update data paths and checksums * bismark/deduplicate: update data paths and checksums * remove obsolete testdata * remove empty 'dummy_file.txt' * update data/README.md * methyldackel: fix test * Revert "methyldackel: fix test" This reverts commit f175a32d144b1b0bfa0c6885da80c51e3cfe038a. * methyldackel: fix test for real * move test.genome.sizes * changed test names * switched genomic to genome and transcriptome * fix bedtools, blast * fix gtf, tabix, .paf * fix bowtie,bwa,bwameth * fixed: bwa, bwamem, gatk, gffread, quast * fixed bismark and blast * fixed remaining tests * delete bam file Co-authored-by: phue <patrick.huether@gmail.com>
2021-03-04 05:10:57 -05:00
md5sum: 982cbc7d9e38743b9b1037588862b9da
update tests for new config (#384) * update tests for new config * fix quast, update more * more updates! * more tests updated * fix tests, added tabix gff3.gz * Delete main.nf Removing SPAdes from PR to avoid merge conflicts with https://github.com/nf-core/modules/pull/396 Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-01 15:22:06 -04:00
- path: ./output/blast/blast_db/genome.fasta.nin
- path: ./output/blast/blast_db/genome.fasta
Converge test data usage (#249) * initial data restructuing * fixed bedtools_complement * fixed bedtools_genomecov * fixed bedtools_getfasta * fixed bedtools_intersect * fixed bedtools maskfasta * fixed bedtools_merge * fixed bedtools_slop * fixed bedtools_sort * fixed bismark_genome_preparation * fixed blast * fixed bowtie data * fixed bowtie2 data * fixed bwa data * fixed bwamem2 data usage * fixed cat_fastq data * fixed cutadapt data * fixed dsh data * fixed fastp data * fixed fastqc; fixed bug with wrong fastq format * fixed gatk * fixed data for gffread, gunzip * fixed ivar paths * fixed data paths for minimap2 * fixed mosdepth * fixed multiqc, pangolin * fixed picard data paths * fixed data paths for qualimap, quast * fixed salmon data paths * fixed samtools paths * fixed seqwish, stringtie paths * fixed tabix, trimgalore paths * cleaned up data * added first description to README * changed test data naming again; everything up to bwa fixed * everything up to gatk4 * fixed everything up to ivar * fixed everything up to picard * everything up to quast * everything fixed up to stringtie * switched everyting to 'test' naming scheme * fixed samtools and ivar tests * cleaned up README a bit * add (simulated) methylation test data based on SARS-CoV-2 genome; simulated with Sherman --non_dir --genome sarscov2/fasta/ --paired -n 10000 -l 100 --CG 20 --CH 90 * bwameth/align: update data paths and checksums also, build index on the go * bwameth/index: update data paths and checksums * methyldackel/extract: update data paths and checksums * methyldackel/mbias: update data paths and checksums * bismark/deduplicate: update data paths and checksums * remove obsolete testdata * remove empty 'dummy_file.txt' * update data/README.md * methyldackel: fix test * Revert "methyldackel: fix test" This reverts commit f175a32d144b1b0bfa0c6885da80c51e3cfe038a. * methyldackel: fix test for real * move test.genome.sizes * changed test names * switched genomic to genome and transcriptome * fix bedtools, blast * fix gtf, tabix, .paf * fix bowtie,bwa,bwameth * fixed: bwa, bwamem, gatk, gffread, quast * fixed bismark and blast * fixed remaining tests * delete bam file Co-authored-by: phue <patrick.huether@gmail.com>
2021-03-04 05:10:57 -05:00
md5sum: 6e9fe4042a72f2345f644f239272b7e6
update tests for new config (#384) * update tests for new config * fix quast, update more * more updates! * more tests updated * fix tests, added tabix gff3.gz * Delete main.nf Removing SPAdes from PR to avoid merge conflicts with https://github.com/nf-core/modules/pull/396 Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-01 15:22:06 -04:00
- path: ./output/blast/blast_db/genome.fasta.nhr
Converge test data usage (#249) * initial data restructuing * fixed bedtools_complement * fixed bedtools_genomecov * fixed bedtools_getfasta * fixed bedtools_intersect * fixed bedtools maskfasta * fixed bedtools_merge * fixed bedtools_slop * fixed bedtools_sort * fixed bismark_genome_preparation * fixed blast * fixed bowtie data * fixed bowtie2 data * fixed bwa data * fixed bwamem2 data usage * fixed cat_fastq data * fixed cutadapt data * fixed dsh data * fixed fastp data * fixed fastqc; fixed bug with wrong fastq format * fixed gatk * fixed data for gffread, gunzip * fixed ivar paths * fixed data paths for minimap2 * fixed mosdepth * fixed multiqc, pangolin * fixed picard data paths * fixed data paths for qualimap, quast * fixed salmon data paths * fixed samtools paths * fixed seqwish, stringtie paths * fixed tabix, trimgalore paths * cleaned up data * added first description to README * changed test data naming again; everything up to bwa fixed * everything up to gatk4 * fixed everything up to ivar * fixed everything up to picard * everything up to quast * everything fixed up to stringtie * switched everyting to 'test' naming scheme * fixed samtools and ivar tests * cleaned up README a bit * add (simulated) methylation test data based on SARS-CoV-2 genome; simulated with Sherman --non_dir --genome sarscov2/fasta/ --paired -n 10000 -l 100 --CG 20 --CH 90 * bwameth/align: update data paths and checksums also, build index on the go * bwameth/index: update data paths and checksums * methyldackel/extract: update data paths and checksums * methyldackel/mbias: update data paths and checksums * bismark/deduplicate: update data paths and checksums * remove obsolete testdata * remove empty 'dummy_file.txt' * update data/README.md * methyldackel: fix test * Revert "methyldackel: fix test" This reverts commit f175a32d144b1b0bfa0c6885da80c51e3cfe038a. * methyldackel: fix test for real * move test.genome.sizes * changed test names * switched genomic to genome and transcriptome * fix bedtools, blast * fix gtf, tabix, .paf * fix bowtie,bwa,bwameth * fixed: bwa, bwamem, gatk, gffread, quast * fixed bismark and blast * fixed remaining tests * delete bam file Co-authored-by: phue <patrick.huether@gmail.com>
2021-03-04 05:10:57 -05:00
md5sum: f4b4ddb034fd3dd7b25c89e9d50c004e
update tests for new config (#384) * update tests for new config * fix quast, update more * more updates! * more tests updated * fix tests, added tabix gff3.gz * Delete main.nf Removing SPAdes from PR to avoid merge conflicts with https://github.com/nf-core/modules/pull/396 Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-01 15:22:06 -04:00
- path: ./output/blast/blast_db/genome.fasta.ndb
nf-core modules bump-versions for all modules (#630) * Add blacklist of modules that shouldn't be updated to .nf-core.yml * nf-core modules bump-versions for all modules * Remove TODO statements identified by linting * Fix md5sums for failing tests * Fix more tests
2021-07-28 04:10:44 -04:00
md5sum: 0d553c830656469211de113c5022f06d
update tests for new config (#384) * update tests for new config * fix quast, update more * more updates! * more tests updated * fix tests, added tabix gff3.gz * Delete main.nf Removing SPAdes from PR to avoid merge conflicts with https://github.com/nf-core/modules/pull/396 Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-01 15:22:06 -04:00
- path: ./output/blast/blast_db/genome.fasta.not
Adding blast blastn module
2021-02-09 10:58:36 -05:00
md5sum: 1e53e9d08f1d23af0299cfa87478a7bb
update tests for new config (#384) * update tests for new config * fix quast, update more * more updates! * more tests updated * fix tests, added tabix gff3.gz * Delete main.nf Removing SPAdes from PR to avoid merge conflicts with https://github.com/nf-core/modules/pull/396 Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-01 15:22:06 -04:00
- path: ./output/blast/blast_db/genome.fasta.nto
Converge test data usage (#249) * initial data restructuing * fixed bedtools_complement * fixed bedtools_genomecov * fixed bedtools_getfasta * fixed bedtools_intersect * fixed bedtools maskfasta * fixed bedtools_merge * fixed bedtools_slop * fixed bedtools_sort * fixed bismark_genome_preparation * fixed blast * fixed bowtie data * fixed bowtie2 data * fixed bwa data * fixed bwamem2 data usage * fixed cat_fastq data * fixed cutadapt data * fixed dsh data * fixed fastp data * fixed fastqc; fixed bug with wrong fastq format * fixed gatk * fixed data for gffread, gunzip * fixed ivar paths * fixed data paths for minimap2 * fixed mosdepth * fixed multiqc, pangolin * fixed picard data paths * fixed data paths for qualimap, quast * fixed salmon data paths * fixed samtools paths * fixed seqwish, stringtie paths * fixed tabix, trimgalore paths * cleaned up data * added first description to README * changed test data naming again; everything up to bwa fixed * everything up to gatk4 * fixed everything up to ivar * fixed everything up to picard * everything up to quast * everything fixed up to stringtie * switched everyting to 'test' naming scheme * fixed samtools and ivar tests * cleaned up README a bit * add (simulated) methylation test data based on SARS-CoV-2 genome; simulated with Sherman --non_dir --genome sarscov2/fasta/ --paired -n 10000 -l 100 --CG 20 --CH 90 * bwameth/align: update data paths and checksums also, build index on the go * bwameth/index: update data paths and checksums * methyldackel/extract: update data paths and checksums * methyldackel/mbias: update data paths and checksums * bismark/deduplicate: update data paths and checksums * remove obsolete testdata * remove empty 'dummy_file.txt' * update data/README.md * methyldackel: fix test * Revert "methyldackel: fix test" This reverts commit f175a32d144b1b0bfa0c6885da80c51e3cfe038a. * methyldackel: fix test for real * move test.genome.sizes * changed test names * switched genomic to genome and transcriptome * fix bedtools, blast * fix gtf, tabix, .paf * fix bowtie,bwa,bwameth * fixed: bwa, bwamem, gatk, gffread, quast * fixed bismark and blast * fixed remaining tests * delete bam file Co-authored-by: phue <patrick.huether@gmail.com>
2021-03-04 05:10:57 -05:00
md5sum: 33cdeccccebe80329f1fdbee7f5874cb
update tests for new config (#384) * update tests for new config * fix quast, update more * more updates! * more tests updated * fix tests, added tabix gff3.gz * Delete main.nf Removing SPAdes from PR to avoid merge conflicts with https://github.com/nf-core/modules/pull/396 Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-01 15:22:06 -04:00
- path: ./output/blast/blast_db/genome.fasta.ntf
nf-core modules bump-versions for all modules (#630) * Add blacklist of modules that shouldn't be updated to .nf-core.yml * nf-core modules bump-versions for all modules * Remove TODO statements identified by linting * Fix md5sums for failing tests * Fix more tests
2021-07-28 04:10:44 -04:00
md5sum: de1250813f0c7affc6d12dac9d0fb6bb
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