Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 33:0a65e6fde7b6

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"planemo upload"
author kkonganti
date Wed, 29 Jun 2022 14:59:22 -0400
parents 9c06429a2ffb
children 1d6557e7db72
comparison
equal deleted inserted replaced
32:9c06429a2ffb 33:0a65e6fde7b6
13 pwd_path=\$(pwd); 13 pwd_path=\$(pwd);
14 $__tool_directory__/0.2.1/cpipes 14 $__tool_directory__/0.2.1/cpipes
15 --pipeline $pipeline 15 --pipeline $pipeline
16 #if ($pipeline == "centriflaken"): 16 #if ($pipeline == "centriflaken"):
17 --fq_single_end true 17 --fq_single_end true
18 --flye_genome_size '${genome_size}'
19 #if ($long_read_platform == "nanopore_corr"):
20 --flye_nano_corr true --flye_nano_raw false
21 #elif ($long_read_platform == "nanopore_hq"):
22 --flye_nano_hq true --flye_nano_raw false
23 #elif ($long_read_platform == "pacbio_raw"):
24 --flye_pacbio_raw true --flye_nano_raw false
25 #elif ($long_read_platform == "pacbio_corr"):
26 --flye_pacbio_corr true --flye_nano_raw false
27 #elif ($long_read_platform == "pacbio_hifi"):
28 --flye_pacbio_hifi true --flye_nano_raw false
29 #end if
18 #elif ($pipeline == "centriflaken_hy"): 30 #elif ($pipeline == "centriflaken_hy"):
19 #if ($reads_lib_layout == "single"): 31 #if ($reads_lib_layout == "single"):
20 --fq_single_end true 32 --fq_single_end true
21 #elif ($reads_lib_layout == "paired"): 33 #elif ($reads_lib_layout == "paired"):
22 --fq_single_end false --fq2_suffix '${fq2_suffix}' 34 --fq_single_end false --fq2_suffix '${fq2_suffix}'
26 --output \${pwd_path}/cpipes-output 38 --output \${pwd_path}/cpipes-output
27 --fq_suffix '${fq_suffix}' 39 --fq_suffix '${fq_suffix}'
28 --fq_filename_delim '${fq_filename_delim}' 40 --fq_filename_delim '${fq_filename_delim}'
29 --fq_filename_delim_idx $fq_filename_delim_idx 41 --fq_filename_delim_idx $fq_filename_delim_idx
30 --centrifuge_extract_bug '${centrifuge_extract_bug}' 42 --centrifuge_extract_bug '${centrifuge_extract_bug}'
31 --flye_genome_size '${genome_size}'
32 #if ($long_read_platform == "nanopore_corr"):
33 --flye_nano_corr true --flye_nano_raw false
34 #elif ($long_read_platform == "nanopore_hq"):
35 --flye_nano_hq true --flye_nano_raw false
36 #elif ($long_read_platform == "pacbio_raw"):
37 --flye_pacbio_raw true --flye_nano_raw false
38 #elif ($long_read_platform == "pacbio_corr"):
39 --flye_pacbio_corr true --flye_nano_raw false
40 #elif ($long_read_platform == "pacbio_hifi"):
41 --flye_pacbio_hifi true --flye_nano_raw false
42 #end if
43 -profile $runtime_profile 43 -profile $runtime_profile
44 -resume; 44 -resume;
45 mv './cpipes-output/${pipeline}-multiqc/multiqc_report.html' './multiqc_report.html'; 45 mv './cpipes-output/${pipeline}-multiqc/multiqc_report.html' './multiqc_report.html';
46 mv './cpipes-output/${pipeline}-results/kraken2_extract_contigs' kraken2_extract_contigs; 46 mv './cpipes-output/${pipeline}-results/kraken2_extract_contigs' kraken2_extract_contigs;
47 ]]></command> 47 ]]></command>