CI
90a16ac646
Build pipeline: viash-hub.biobox.add-agat-convert-spgff2tsv-t5ds2
Source commit: fa5ed706e5
Source message: add tests
106 lines
5.9 KiB
Bash
106 lines
5.9 KiB
Bash
#!/bin/bash
|
|
|
|
## VIASH START
|
|
## VIASH END
|
|
|
|
# disable flags
|
|
[[ "$par_disable_adapter_trimming" == "false" ]] && unset par_disable_adapter_trimming
|
|
[[ "$par_detect_adapter_for_pe" == "false" ]] && unset par_detect_adapter_for_pe
|
|
[[ "$par_merge" == "false" ]] && unset par_merge
|
|
[[ "$par_include_unmerged" == "false" ]] && unset par_include_unmerged
|
|
[[ "$par_interleaved_in" == "false" ]] && unset par_interleaved_in
|
|
[[ "$par_fix_mgi_id" == "false" ]] && unset par_fix_mgi_id
|
|
[[ "$par_phred64" == "false" ]] && unset par_phred64
|
|
[[ "$par_dont_overwrite" == "false" ]] && unset par_dont_overwrite
|
|
[[ "$par_verbose" == "false" ]] && unset par_verbose
|
|
[[ "$par_dedup" == "false" ]] && unset par_dedup
|
|
[[ "$par_dont_eval_duplication" == "false" ]] && unset par_dont_eval_duplication
|
|
[[ "$par_trim_poly_g" == "false" ]] && unset par_trim_poly_g
|
|
[[ "$par_disable_trim_poly_g" == "false" ]] && unset par_disable_trim_poly_g
|
|
[[ "$par_trim_poly_x" == "false" ]] && unset par_trim_poly_x
|
|
[[ "$par_disable_quality_filtering" == "false" ]] && unset par_disable_quality_filtering
|
|
[[ "$par_disable_length_filtering" == "false" ]] && unset par_disable_length_filtering
|
|
[[ "$par_low_complexity_filter" == "false" ]] && unset par_low_complexity_filter
|
|
[[ "$par_umi" == "false" ]] && unset par_umi
|
|
[[ "$par_overrepresentation_analysis" == "false" ]] && unset par_overrepresentation_analysis
|
|
|
|
# run command
|
|
fastp \
|
|
-i "$par_in1" \
|
|
-o "$par_out1" \
|
|
${par_in2:+--in2 "${par_in2}"} \
|
|
${par_out2:+--out2 "${par_out2}"} \
|
|
${par_unpaired1:+--unpaired1 "${par_unpaired1}"} \
|
|
${par_unpaired2:+--unpaired2 "${par_unpaired2}"} \
|
|
${par_failed_out:+--failed_out "${par_failed_out}"} \
|
|
${par_overlapped_out:+--overlapped_out "${par_overlapped_out}"} \
|
|
${par_json:+--json "${par_json}"} \
|
|
${par_html:+--html "${par_html}"} \
|
|
${par_report_title:+--report_title "${par_report_title}"} \
|
|
${par_disable_adapter_trimming:+--disable_adapter_trimming} \
|
|
${par_detect_adapter_for_pe:+--detect_adapter_for_pe} \
|
|
${par_adapter_sequence:+--adapter_sequence "${par_adapter_sequence}"} \
|
|
${par_adapter_sequence_r2:+--adapter_sequence_r2 "${par_adapter_sequence_r2}"} \
|
|
${par_adapter_fasta:+--adapter_fasta "${par_adapter_fasta}"} \
|
|
${par_trim_front1:+--trim_front1 "${par_trim_front1}"} \
|
|
${par_trim_tail1:+--trim_tail1 "${par_trim_tail1}"} \
|
|
${par_max_len1:+--max_len1 "${par_max_len1}"} \
|
|
${par_trim_front2:+--trim_front2 "${par_trim_front2}"} \
|
|
${par_trim_tail2:+--trim_tail2 "${par_trim_tail2}"} \
|
|
${par_max_len2:+--max_len2 "${par_max_len2}"} \
|
|
${par_merge:+--merge} \
|
|
${par_merged_out:+--merged_out "${par_merged_out}"} \
|
|
${par_include_unmerged:+--include_unmerged} \
|
|
${par_interleaved_in:+--interleaved_in} \
|
|
${par_fix_mgi_id:+--fix_mgi_id} \
|
|
${par_phred64:+--phred64} \
|
|
${par_compression:+--compression "${par_compression}"} \
|
|
${par_dont_overwrite:+--dont_overwrite} \
|
|
${par_verbose:+--verbose} \
|
|
${par_reads_to_process:+--reads_to_process "${par_reads_to_process}"} \
|
|
${par_dedup:+--dedup} \
|
|
${par_dup_calc_accuracy:+--dup_calc_accuracy "${par_dup_calc_accuracy}"} \
|
|
${par_dont_eval_duplication:+--dont_eval_duplication} \
|
|
${par_trim_poly_g:+--trim_poly_g} \
|
|
${par_poly_g_min_len:+--poly_g_min_len "${par_poly_g_min_len}"} \
|
|
${par_disable_trim_poly_g:+--disable_trim_poly_g} \
|
|
${par_trim_poly_x:+--trim_poly_x} \
|
|
${par_poly_x_min_len:+--poly_x_min_len "${par_poly_x_min_len}"} \
|
|
${par_cut_front:+--cut_front "${par_cut_front}"} \
|
|
${par_cut_tail:+--cut_tail "${par_cut_tail}"} \
|
|
${par_cut_right:+--cut_right "${par_cut_right}"} \
|
|
${par_cut_window_size:+--cut_window_size "${par_cut_window_size}"} \
|
|
${par_cut_mean_quality:+--cut_mean_quality "${par_cut_mean_quality}"} \
|
|
${par_cut_front_window_size:+--cut_front_window_size "${par_cut_front_window_size}"} \
|
|
${par_cut_front_mean_quality:+--cut_front_mean_quality "${par_cut_front_mean_quality}"} \
|
|
${par_cut_tail_window_size:+--cut_tail_window_size "${par_cut_tail_window_size}"} \
|
|
${par_cut_tail_mean_quality:+--cut_tail_mean_quality "${par_cut_tail_mean_quality}"} \
|
|
${par_cut_right_window_size:+--cut_right_window_size "${par_cut_right_window_size}"} \
|
|
${par_cut_right_mean_quality:+--cut_right_mean_quality "${par_cut_right_mean_quality}"} \
|
|
${par_disable_quality_filtering:+--disable_quality_filtering} \
|
|
${par_qualified_quality_phred:+--qualified_quality_phred "${par_qualified_quality_phred}"} \
|
|
${par_unqualified_percent_limit:+--unqualified_percent_limit "${par_unqualified_percent_limit}"} \
|
|
${par_n_base_limit:+--n_base_limit "${par_n_base_limit}"} \
|
|
${par_average_qual:+--average_qual "${par_average_qual}"} \
|
|
${par_disable_length_filtering:+--disable_length_filtering} \
|
|
${par_length_required:+--length_required "${par_length_required}"} \
|
|
${par_length_limit:+--length_limit "${par_length_limit}"} \
|
|
${par_low_complexity_filter:+--low_complexity_filter} \
|
|
${par_complexity_threshold:+--complexity_threshold "${par_complexity_threshold}"} \
|
|
${par_filter_by_index1:+--filter_by_index1 "${par_filter_by_index1}"} \
|
|
${par_filter_by_index2:+--filter_by_index2 "${par_filter_by_index2}"} \
|
|
${par_filter_by_index_threshold:+--filter_by_index_threshold "${par_filter_by_index_threshold}"} \
|
|
${par_correction:+--correction} \
|
|
${par_overlap_len_require:+--overlap_len_require "${par_overlap_len_require}"} \
|
|
${par_overlap_diff_limit:+--overlap_diff_limit "${par_overlap_diff_limit}"} \
|
|
${par_overlap_diff_percent_limit:+--overlap_diff_percent_limit "${par_overlap_diff_percent_limit}"} \
|
|
${par_umi:+--umi} \
|
|
${par_umi_loc:+--umi_loc "${par_umi_loc}"} \
|
|
${par_umi_len:+--umi_len "${par_umi_len}"} \
|
|
${par_umi_prefix:+--umi_prefix "${par_umi_prefix}"} \
|
|
${par_umi_skip:+--umi_skip "${par_umi_skip}"} \
|
|
${par_umi_delim:+--umi_delim "${par_umi_delim}"} \
|
|
${par_overrepresentation_analysis:+--overrepresentation_analysis} \
|
|
${par_overrepresentation_sampling:+--overrepresentation_sampling "${par_overrepresentation_sampling}"} \
|
|
${meta_cpus:+--thread "${meta_cpus}"}
|