Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 125:dcd41789fb61

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload
author kkonganti
date Wed, 03 Jul 2024 13:11:34 -0400
parents 45ccd0403784
children 9cf321470e20
comparison
equal deleted inserted replaced
124:45ccd0403784 125:dcd41789fb61
36 ln -sf '$pair.reverse' "\${input_path}/$read_R2"; 36 ln -sf '$pair.reverse' "\${input_path}/$read_R2";
37 #end for 37 #end for
38 #end if 38 #end if
39 nextflow /galaxy/cfsan-centriflaken-db/0.4.2/cpipes 39 nextflow /galaxy/cfsan-centriflaken-db/0.4.2/cpipes
40 --pipeline $input_read_type_cond.pipeline_cond.pipeline 40 --pipeline $input_read_type_cond.pipeline_cond.pipeline
41 -work-dir \${work_dir}
42 #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"): 41 #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"):
43 --fq_single_end true 42 --fq_single_end true
44 --flye_genome_size '${genome_size}' 43 --flye_genome_size '${genome_size}'
45 #if ($input_read_type_cond.pipeline_cond.long_read_platform == "nanopore_corr"): 44 #if ($input_read_type_cond.pipeline_cond.long_read_platform == "nanopore_corr"):
46 --flye_nano_corr true --flye_nano_raw false 45 --flye_nano_corr true --flye_nano_raw false
70 --fq_filename_delim_idx $fq_filename_delim_idx 69 --fq_filename_delim_idx $fq_filename_delim_idx
71 --centrifuge_extract_bug '${centrifuge_extract_bug}' 70 --centrifuge_extract_bug '${centrifuge_extract_bug}'
72 #if (str($input_read_type_cond.pipeline_cond.rm_dup_seqs) == "true"): 71 #if (str($input_read_type_cond.pipeline_cond.rm_dup_seqs) == "true"):
73 --seqkit_rmdup_run true 72 --seqkit_rmdup_run true
74 #end if 73 #end if
74 -work-dir \${work_dir}
75 -profile gxkubernetes; 75 -profile gxkubernetes;
76 mv "\${work_dir}/cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/multiqc_report.html" './multiqc_report.html' > /dev/null 2>&1 || exit 1; 76 mv "\${work_dir}/cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/multiqc_report.html" './multiqc_report.html' > /dev/null 2>&1 || exit 1;
77 mv "\${work_dir}/cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-results/kraken2_extract_contigs" kraken2_extract_contigs > /dev/null 2>&1 || exit 1; 77 mv "\${work_dir}/cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-results/kraken2_extract_contigs" kraken2_extract_contigs > /dev/null 2>&1 || exit 1;
78 rm -rf "\${work_dir}/cpipes-output" > /dev/null 2>&1 || exit 1; 78 rm -rf "\${work_dir}/cpipes-output" > /dev/null 2>&1 || exit 1;
79 ]]></command> 79 ]]></command>