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Merge pull request #35 from sanger-tol/dp24_organellar
Dp24 organellar
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,22 +1,24 @@ | ||
| assembly_path: /lustre/scratch123/tol/resources/treeval/treeval-testdata/asccTinyTest/assembly/Pyoeliiyoelii17XNL_assembly.fa | ||
| assembly_path: /nfs/treeoflife-01/teams/tola/users/dp24/ascc/ncbi_dataset/data/reheadered.fna | ||
| assembly_title: asccTinyTest | ||
| pacbio_barcodes: /nfs/treeoflife-01/teams/tola/users/dp24/ascc/assets/pacbio_adaptors.fa | ||
| pacbio_multiplexing_barcode_names: "bc1008,bc1009" | ||
| pacbio_reads_path: /lustre/scratch123/tol/resources/treeval/treeval-testdata/asccTinyTest/pacbio/ | ||
| pacbio_reads_path: /nfs/treeoflife-01/teams/tola/users/dp24/ascc/asccTinyTest/pacbio/ | ||
| sci_name: "Plasmodium yoelii yoelii 17XNL" | ||
| taxid: 352914 | ||
| mito_fasta_path: /lustre/scratch123/tol/resources/treeval/treeval-testdata/asccTinyTest/organellar/Pyoeliiyoelii17XNL_mitochondrion_ncbi.fa | ||
| plastid_fasta_path: /lustre/scratch123/tol/resources/treeval/treeval-testdata/asccTinyTest/organellar/Pyoeliiyoelii17XNL_apicoplast_ncbi.fa | ||
| mito_fasta_path: /nfs/treeoflife-01/teams/tola/users/dp24/ascc/asccTinyTest/organellar/Pyoeliiyoelii17XNL_mitochondrion_ncbi.fa | ||
| plastid_fasta_path: /nfs/treeoflife-01/teams/tola/users/dp24/ascc/asccTinyTest/organellar/Pyoeliiyoelii17XNL_apicoplast_ncbi.fa | ||
| kmer_len: 7 | ||
| nt_database: /data/blastdb/Supported/NT/current/ | ||
| nt_database: /data/blastdb/Supported/NT/202308/dbv4/ | ||
| nt_database_prefix: nt | ||
| nt_kraken_db_path: /lustre/scratch123/tol/teams/tola/users/ea10/ascc_databases/nt/nt | ||
| ncbi_accessionids_folder: /lustre/scratch123/tol/teams/tola/users/ea10/ascc_databases/ncbi_taxonomy/20230509_accession2taxid/ | ||
| ncbi_taxonomy_path: /lustre/scratch123/tol/teams/tola/users/ea10/databases/taxdump/ | ||
| ncbi_rankedlineage_path: /lustre/scratch123/tol/teams/tola/users/ea10/databases/taxdump/rankedlineage.dmp | ||
| busco_lineages_folder: /lustre/scratch123/tol/resources/busco/data/v5/2021-03-14/lineages | ||
| busco_lineages_folder: /lustre/scratch123/tol/resources/busco/data/v5/2021-08-27/lineages | ||
| fcs_gx_database_path: /lustre/scratch124/tol/projects/asg/sub_projects/ncbi_decon/0.4.0/gxdb | ||
| vecscreen_database_path: /lustre/scratch123/tol/teams/tola/users/ea10/ascc_databases/vecscreen_database/adaptors_for_screening_euks.fa | ||
| diamond_uniprot_database_path: /lustre/scratch123/tol/teams/tola/users/ea10/ascc_databases/uniprot/uniprot_reference_proteomes_with_taxonnames.dmnd | ||
| diamond_nr_database_path: /lustre/scratch123/tol/teams/tola/users/ea10/ascc_databases/proteins2/nr.dmnd | ||
| diamond_nr_database_path: /lustre/scratch123/tol/resources/nr/latest/nr.dmnd | ||
| seqkit: | ||
| sliding: 6000 | ||
| window: 100000 | ||
| sliding: 100000 | ||
| window: 6000 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,50 @@ | ||
| process BLAST_V5_DATABASE { | ||
| tag "$meta.id" | ||
| label 'process_medium' | ||
|
|
||
| conda "bioconda::blast=2.14.1" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/blast:2.14.1--pl5321h6f7f691_0': | ||
| 'biocontainers/blast:2.14.1--pl5321h6f7f691_0' }" | ||
|
|
||
| input: | ||
| tuple val(meta), path(fasta) | ||
| path db | ||
| val db_prefix | ||
|
|
||
| output: | ||
| tuple val(meta), path('*.txt'), emit: txt | ||
| path "versions.yml" , emit: versions | ||
|
|
||
| when: | ||
| task.ext.when == null || task.ext.when | ||
|
|
||
| script: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| """ | ||
| blastn \\ | ||
| -num_threads $task.cpus \\ | ||
| -db ${db}/${db_prefix} \\ | ||
| -query $fasta \\ | ||
| $args \\ | ||
| -out ${prefix}.txt | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| blast: \$(blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\$//') | ||
| END_VERSIONS | ||
| """ | ||
|
|
||
| stub: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| """ | ||
| touch ${prefix}.txt | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| blast: \$(blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\$//') | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,43 @@ | ||
| process FILTER_COMMENTS { | ||
| tag "${meta.id}" | ||
| label 'process_low' | ||
|
|
||
| conda "conda-forge::coreutils=9.1" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : | ||
| 'docker.io/ubuntu:20.04' }" | ||
|
|
||
| input: | ||
| tuple val(meta), path(busco) | ||
|
|
||
| output: | ||
| tuple val(meta), path( "*txt" ) , emit: txt | ||
| path "versions.yml" , emit: versions | ||
|
|
||
| script: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| def VERSION = "9.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. | ||
| """ | ||
| cat ${busco} | awk '\$4>=200' | grep -v '#' > ${prefix}_filtered_busco.txt | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| ubuntu: \$(ubuntu --version | sed 's/Ubuntu //g') | ||
| coreutils: $VERSION | ||
| END_VERSIONS | ||
| """ | ||
|
|
||
| stub: | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| def VERSION = "9.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. | ||
| """ | ||
| touch ${prefix}.fa | ||
| cat <<-END_VERSIONS > ${prefix}_filtered_busco.txt | ||
| "${task.process}": | ||
| ubuntu: \$(ubuntu --version | sed 's/Ubuntu //g') | ||
| coreutils: $VERSION | ||
| END_VERSIONS | ||
| """ | ||
| } |
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