8000 Test full by jma1991 · Pull Request #48 · nf-core/rnasplice · GitHub
[go: up one dir, main page]
More Web Proxy on the site http://driver.im/
Skip to content

Test full #48

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 2 commits into from
Mar 21, 2023
Merged

Test full #48

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
f9d2528
update test configs
jma1991 Mar 17, 2023
6037411
update conf profiles
jma1991 Mar 21, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
15 changes: 8 additions & 7 deletions conf/test.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,24 +11,25 @@
*/

params {

// Config information
config_profile_name = 'Test profile'
config_profile_description = 'Minimal test dataset to check pipeline function'

// Limit resources so that this can run on GitHub Actions

max_cpus = 1
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'

// Input data human chr X from hisat2 stringtie

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnasplice/samplesheet/samplesheet.csv'

// Genome references human chr X from hisat2 stringtie

// Genome references
fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnasplice/reference/X.fa.gz'
gtf = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnasplice/reference/genes_chrX.gtf'

pseudo_aligner = 'salmon'
// Other parameters
deu_lfc_denominator = 'GBR'
dtu_lfc_denominator = 'GBR'

}
39 changes: 12 additions & 27 deletions conf/test_dexseq.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,43 +11,28 @@
*/

params {

// Config information
config_profile_name = 'Test profile'
config_profile_description = 'Minimal test dataset to check pipeline function'
config_profile_description = 'Minimal test dataset to check DEXSeq subworkflow'

// Limit resources so that this can run on GitHub Actions

max_cpus = 1
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'

// Input data human chr X from hisat2 stringtie

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnasplice/samplesheet/samplesheet.csv'

// Genome references human chr X from hisat2 stringtie

// Genome references
fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnasplice/reference/X.fa.gz'
gtf = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnasplice/reference/genes_chrX.gtf'

// DEXSeq DEU
dexseq_exon = true
save_dexseq_annotation = true
gff_dexseq = null
alignment_quality = 10
aggregation = true
deu_lfc_denominator = "GBR"

// DEXSeq DTU
dexseq_dtu = true
dtu_txi = 'dtuScaledTPM' // dtuScaledTPM or scaledTPM
dtu_lfc_denominator = "GBR"

// Additional
aligner = 'star'
pseudo_aligner = 'salmon'
skip_alignment = false
rmats = false
edger_exon = false
suppa = false
// Other parameters
deu_lfc_denominator = "GBR"
dtu_lfc_denominator = "GBR"
rmats = false
edger_exon = false
suppa = false

}
26 changes: 12 additions & 14 deletions conf/test_edger.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,31 +11,29 @@
*/

params {

// Config information
config_profile_name = 'Test profile'
config_profile_description = 'Minimal test dataset to check pipeline function'
config_profile_description = 'Minimal test dataset to check edgeR subworkflow'

// Limit resources so that this can run on GitHub Actions

max_cpus = 1
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'

// Input data human chr X from hisat2 stringtie

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnasplice/samplesheet/samplesheet.csv'

// Genome references human chr X from hisat2 stringtie

// Genome references
fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnasplice/reference/X.fa.gz'
gtf = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnasplice/reference/genes_chrX.gtf'

aligner = 'star'
// Other parameters
pseudo_aligner = false
skip_alignment = false
rmats = false
dexseq_exon = false
edger_exon = true
dexseq_dtu = false
suppa = false
rmats = false
dexseq_exon = false
edger_exon = true
dexseq_dtu = false
suppa = false

}
10000
12 changes: 10 additions & 2 deletions conf/test_full.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,11 +11,19 @@
*/

params {

// Config information
config_profile_name = 'Full test profile'
config_profile_description = 'Full test dataset to check pipeline function'

// Input data for full size test
// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnasplice/samplesheet/samplesheet_full.csv'

// Genome references
genome = 'GRCh37'
pseudo_aligner = 'salmon'

// Other parameters
deu_lfc_denominator = 'PC3E'
dtu_lfc_denominator = 'PC3E'

}
34 changes: 11 additions & 23 deletions conf/test_rmats.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,40 +11,28 @@
*/

params {

// Config information
config_profile_name = 'Test profile'
config_profile_description = 'Minimal test dataset to check pipeline function'
config_profile_description = 'Minimal test dataset to check rMATS subworkflow'

// Limit resources so that this can run on GitHub Actions

max_cpus = 1
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'

// Input data human chr X from hisat2 stringtie

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnasplice/samplesheet/samplesheet.csv'

// Genome references human chr X from hisat2 stringtie

// Genome references
fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnasplice/reference/X.fa.gz'
gtf = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnasplice/reference/genes_chrX.gtf'

// rMATs
rmats = true
rmats_splice_diff_cutoff = 0.0001
rmats_paired_stats = true
rmats_read_len = 40
rmats_novel_splice_site = false
rmats_min_intron_len = 50
rmats_max_exon_len = 500

// Additional
aligner = 'star'
// Other parameters
pseudo_aligner = false
skip_alignment = false
dexseq_exon = false
edger_exon = false
dexseq_dtu = false
suppa = false
dexseq_exon = false
edger_exon = false
dexseq_dtu = false
suppa = false

}
55 changes: 7 additions & 48 deletions conf/test_suppa.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,66 +11,25 @@
*/

params {

// Config information
config_profile_name = 'Test profile'
config_profile_description = 'Minimal test dataset to check pipeline function'
config_profile_description = 'Minimal test dataset to check SUPPA subworkflow'

// Limit resources so that this can run on GitHub Actions

max_cpus 9E7A = 1
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'

// Input data human chr X from hisat2 stringtie

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnasplice/samplesheet/samplesheet.csv'

// Genome references human chr X from hisat2 stringtie

// Genome references
fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnasplice/reference/X.fa.gz'
gtf = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnasplice/reference/genes_chrX.gtf'

// SUPPA options
suppa = true
suppa_per_local_event = true
suppa_per_isoform = true
suppa_tpm = null

// SUPPA Generate events options
generateevents_pool_genes = true
generateevents_event_type = 'SE SS MX RI FL'
generateevents_boundary = 'S'
generateevents_threshold = 10
generateevents_exon_length = 100
psiperevent_total_filter = 0

// SUPPA Diffsplice options
diffsplice_local_event = true
diffsplice_isoform = true
diffsplice_method = 'empirical'
diffsplice_area = 1000
diffsplice_lower_bound = 0
diffsplice_gene_correction = true
diffsplice_paired = true
diffsplice_alpha = 0.05
diffsplice_median = false
diffsplice_tpm_threshold = 0
diffsplice_nan_threshold = 0

// SUPPA Cluster options
clusterevents_local_event = true
clusterevents_isoform = true
clusterevents_sigthreshold = null
clusterevents_dpsithreshold= 0.05
clusterevents_eps = 0.05
clusterevents_metric = 'euclidean'
clusterevents_separation = null
clusterevents_min_pts = 20
clusterevents_method = 'DBSCAN'

// Additional
// Other parameters
aligner = 'star_salmon'
pseudo_aligner = 'salmon'
skip_alignment = false
rmats = false
dexseq_exon = false
edger_exon = false
Expand Down
Loading
0