workflow-generate-dataset-for-assembly-tutorial

Associated Tutorial

This workflows is part of the tutorial workflow-generate-dataset-for-assembly-tutorial, available in the GTN

Tutorial Author(s): Polina Polunina, Bérénice Batut

Funder(s): Gallantries: Bridging Training Communities in Life Science, Environment and Health

Inputs

ID	Name	Description	Type
ERR2231567_1.fastq.gz	#main/ERR2231567_1.fastq.gz	n/a	File
ERR2231567_2.fastq.gz	#main/ERR2231567_2.fastq.gz	n/a	File

Steps

ID	Name	Description
2	Cutadapt	toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0
3	MEGAHIT	toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0
4	Bowtie2	toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1
5	BAM filter	toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9
6	BAM filter	toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9
7	Convert, Merge, Randomize	toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0
8	Convert, Merge, Randomize	toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0
9	Select random lines	random_lines1
10	Select random lines	random_lines1
11	Filter Tabular	toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0
12	Filter Tabular	toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0
13	Unique	toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3
14	Unique	toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3
15	Concatenate datasets	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1
16	seqtk_subseq	toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1
17	seqtk_subseq	toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1
18	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0
19	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0

Outputs

ID	Name	Description	Type
_anonymous_output_1	#main/_anonymous_output_1	n/a	File
_anonymous_output_10	#main/_anonymous_output_10	n/a	File
_anonymous_output_11	#main/_anonymous_output_11	n/a	File
_anonymous_output_12	#main/_anonymous_output_12	n/a	File
_anonymous_output_13	#main/_anonymous_output_13	n/a	File
_anonymous_output_14	#main/_anonymous_output_14	n/a	File
_anonymous_output_15	#main/_anonymous_output_15	n/a	File
_anonymous_output_16	#main/_anonymous_output_16	n/a	File
_anonymous_output_17	#main/_anonymous_output_17	n/a	File
_anonymous_output_18	#main/_anonymous_output_18	n/a	File
_anonymous_output_19	#main/_anonymous_output_19	n/a	File
_anonymous_output_2	#main/_anonymous_output_2	n/a	File
_anonymous_output_20	#main/_anonymous_output_20	n/a	File
_anonymous_output_21	#main/_anonymous_output_21	n/a	File
_anonymous_output_22	#main/_anonymous_output_22	n/a	File
_anonymous_output_23	#main/_anonymous_output_23	n/a	File
_anonymous_output_3	#main/_anonymous_output_3	n/a	File
_anonymous_output_4	#main/_anonymous_output_4	n/a	File
_anonymous_output_5	#main/_anonymous_output_5	n/a	File
_anonymous_output_6	#main/_anonymous_output_6	n/a	File
_anonymous_output_7	#main/_anonymous_output_7	n/a	File
_anonymous_output_8	#main/_anonymous_output_8	n/a	File
_anonymous_output_9	#main/_anonymous_output_9	n/a	File