Nextflow#
Nextflow is a workflow management system used for executing scientific workflows across platforms scalably, portably, and reproducibly.
Here, we’ll run nf-core/rnaseq to process .fastq files from bulk RNA sequencing using STAR, RSEM, HISAT2, Salmon with gene/isoform counts and extensive quality control (reference).
Setup#
Let’s create a test instance:
!lamin init --storage . --name nextflow-bulkrna
Show code cell output
✅ saved: User(id='DzTjkKse', handle='testuser1', email='testuser1@lamin.ai', name='Test User1', updated_at=2023-09-20 21:15:33)
✅ saved: Storage(id='xDVZ4rtk', root='/home/runner/work/nextflow-lamin-usecases/nextflow-lamin-usecases/docs/guide', type='local', updated_at=2023-09-20 21:15:33, created_by_id='DzTjkKse')
💡 loaded instance: testuser1/nextflow-bulkrna
💡 did not register local instance on hub (if you want, call `lamin register`)
import lamindb as ln
from subprocess import getoutput
💡 loaded instance: testuser1/nextflow-bulkrna (lamindb 0.54.0)
Download test data#
Download test data using git:
!git clone https://github.com/nf-core/test-datasets --single-branch --branch rnaseq3 --depth 1
Show code cell output
Cloning into 'test-datasets'...
remote: Enumerating objects: 37, done.
remote: Counting objects: 2% (1/37)
remote: Counting objects: 5% (2/37)
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remote: Counting objects: 100% (37/37), done.
remote: Compressing objects: 2% (1/34)
remote: Compressing objects: 5% (2/34)
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remote: Compressing objects: 100% (34/34), done.
Receiving objects: 2% (1/37)
Receiving objects: 5% (2/37)
Receiving objects: 8% (3/37)
Receiving objects: 10% (4/37)
Receiving objects: 13% (5/37)
Receiving objects: 16% (6/37)
Receiving objects: 18% (7/37)
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Receiving objects: 27% (10/37)
Receiving objects: 29% (11/37)
Receiving objects: 32% (12/37)
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Receiving objects: 43% (16/37)
Receiving objects: 45% (17/37)
Receiving objects: 48% (18/37)
Receiving objects: 48% (18/37), 29.39 MiB | 29.38 MiB/s
Receiving objects: 51% (19/37), 29.39 MiB | 29.38 MiB/s
Receiving objects: 54% (20/37), 29.39 MiB | 29.38 MiB/s
Receiving objects: 56% (21/37), 29.39 MiB | 29.38 MiB/s
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Receiving objects: 64% (24/37), 29.39 MiB | 29.38 MiB/s
Receiving objects: 67% (25/37), 29.39 MiB | 29.38 MiB/s
Receiving objects: 70% (26/37), 29.39 MiB | 29.38 MiB/s
Receiving objects: 72% (27/37), 29.39 MiB | 29.38 MiB/s
Receiving objects: 75% (28/37), 29.39 MiB | 29.38 MiB/s
Receiving objects: 78% (29/37), 29.39 MiB | 29.38 MiB/s
Receiving objects: 81% (30/37), 29.39 MiB | 29.38 MiB/s
Receiving objects: 83% (31/37), 29.39 MiB | 29.38 MiB/s
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Receiving objects: 89% (33/37), 29.39 MiB | 29.38 MiB/s
Receiving objects: 91% (34/37), 29.39 MiB | 29.38 MiB/s
Receiving objects: 94% (35/37), 29.39 MiB | 29.38 MiB/s
Receiving objects: 97% (36/37), 52.55 MiB | 34.89 MiB/s
remote: Total 37 (delta 0), reused 34 (delta 0), pack-reused 0
Receiving objects: 100% (37/37), 52.55 MiB | 34.89 MiB/s
Receiving objects: 100% (37/37), 55.52 MiB | 35.44 MiB/s, done.
Track the download:
download = ln.Transform(name="Download")
download_url = "https://github.com/nf-core/test-datasets"
# create global run containing the download_url
ln.track(download, reference=download_url, reference_type="url")
💡 Transform(id='PS57f9enajyu4R', name='Download', type=notebook, updated_at=2023-09-20 21:15:38, created_by_id='DzTjkKse')
💡 Run(id='7QYShc4f4eh6XDVbM5ou', run_at=2023-09-20 21:15:38, reference='https://github.com/nf-core/test-datasets', reference_type='url', transform_id='PS57f9enajyu4R', created_by_id='DzTjkKse')
Register input files - they’ll automatically be linked against the download run:
sample_sheet = ln.File("test-datasets/samplesheet/v3.10/samplesheet_test.csv")
ln.save(sample_sheet)
input_fastqs = ln.File.from_dir("test-datasets/testdata/GSE110004/")
ln.save(input_fastqs)
Show code cell output
❗ file has more than one suffix (path.suffixes), inferring: '.fastq.gz'
❗ file has more than one suffix (path.suffixes), inferring: '.fastq.gz'
❗ file has more than one suffix (path.suffixes), inferring: '.fastq.gz'
❗ file has more than one suffix (path.suffixes), inferring: '.fastq.gz'
❗ file has more than one suffix (path.suffixes), inferring: '.fastq.gz'
❗ file has more than one suffix (path.suffixes), inferring: '.fastq.gz'
❗ file has more than one suffix (path.suffixes), inferring: '.fastq.gz'
❗ file has more than one suffix (path.suffixes), inferring: '.fastq.gz'
❗ file has more than one suffix (path.suffixes), inferring: '.fastq.gz'
❗ file has more than one suffix (path.suffixes), inferring: '.fastq.gz'
❗ file has more than one suffix (path.suffixes), inferring: '.fastq.gz'
Visualize data lineage for one of the files:
sample_sheet.view_flow()
Track the Nextflow run#
Track the Nextflow workflow & run:
transform = ln.Transform(
name="nf-core rnaseq",
version="3.11.2",
type="pipeline",
reference="https://github.com/laminlabs/nextflow-lamin-usecases",
)
ln.track(transform)
# let's grab the run of the global run context
run = ln.dev.run_context.run
💡 Transform(id='lZgRyrOZ276z6l', name='nf-core rnaseq', version='3.11.2', type='pipeline', reference='https://github.com/laminlabs/nextflow-lamin-usecases', updated_at=2023-09-20 21:15:38, created_by_id='DzTjkKse')
💡 Run(id='SrkbIyjG3uZcZoCLaSfq', run_at=2023-09-20 21:15:38, transform_id='lZgRyrOZ276z6l', created_by_id='DzTjkKse')
If we now stage input files, they’ll be tracked as inputs for the global run:
input_sample_sheet_path = sample_sheet.stage()
input_paths = [input_fastq.stage() for input_fastq in input_fastqs]
Run the nextflow pipeline:
!nextflow run nf-core/rnaseq -r 3.11.2 -profile test,docker --outdir rna-seq-results -name {run.id}
Show code cell output
N E X T F L O W ~ version 23.04.3
Pulling nf-core/rnaseq ...
downloaded from https://github.com/nf-core/rnaseq.git
Launching `https://github.com/nf-core/rnaseq` [SrkbIyjG3uZcZoCLaSfq] DSL2 - revision: 5671b65af9 [3.11.2]
-
----------------------------------------------------
-
,--.
/
,-.
___ __ __ __ ___
/,-._.--~'
|\ | |__ __ / ` / \ |__) |__
} {
| \| | \__, \__/ | \ |___
\`-._,-`-,
`._,._,'
nf-core/rnaseq v3.11.2-g5671b65
-
----------------------------------------------------
-
Core Nextflow options
revision :
3.11.2
runName :
SrkbIyjG3uZcZoCLaSfq
containerEngine :
docker
launchDir :
/home/runner/work/nextflow-lamin-usecases/nextflow-lamin-usecases/docs/guide
workDir :
/home/runner/work/nextflow-lamin-usecases/nextflow-lamin-usecases/docs/guide/work
projectDir :
/home/runner/.nextflow/assets/nf-core/rnaseq
userName :
runner
profile :
test,docker
configFiles :
/home/runner/.nextflow/assets/nf-core/rnaseq/nextflow.config
Input/output options
input :
https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/samplesheet/v3.10/samplesheet_test.csv
outdir :
rna-seq-results
UMI options
umitools_bc_pattern :
NNNN
Read filtering options
bbsplit_fasta_list :
https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/bbsplit_fasta_list.txt
skip_bbsplit :
false
Reference genome options
fasta :
https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/genome.fasta
gtf :
https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/genes.gtf.gz
gff :
https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/genes.gff.gz
transcript_fasta :
https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/transcriptome.fasta
additional_fasta :
https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/gfp.fa.gz
hisat2_index :
https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/hisat2.tar.gz
rsem_index :
https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/rsem.tar.gz
salmon_index :
https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/salmon.tar.gz
Alignment options
pseudo_aligner :
salmon
Institutional config options
config_profile_name :
Test profile
config_profile_description:
Minimal test dataset to check pipeline function
Max job request options
max_cpus :
2
max_memory :
6.GB
max_time :
6.h
!! Only displaying parameters that differ from the pipeline defaults !!
-
----------------------------------------------------
-
If you use nf-core/rnaseq for your analysis please cite:
* The pipeline
https://doi.org/10.5281/zenodo.1400710
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/rnaseq/blob/master/CITATIONS.md
-
----------------------------------------------------
-
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Both '--gtf' and '--gff' parameters have been provided.
Using GTF file as priority.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
'--transcript_fasta' parameter has been provided.
Make sure transcript names in this file match those in the GFF/GTF file.
Please see:
https://github.com/nf-core/rnaseq/issues/753
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[bd/4998a2] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)
[43/b8d09f] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)
[89/260931] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)
[72/d2e426] Submitted process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)
[18/3f69bc] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CAT_ADDITIONAL_FASTA (gfp.fa)
[72/578eb4] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[83/8a605f] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[0a/cdbf1d] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (genome_gfp.fasta)
[17/0cc456] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT
[71/ffa88b] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP2)
[b5/12c6ec] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2)
[42/ebe915] Submitted process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ (WT_REP1)
[48/53803b] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (RAP1_UNINDUCED_REP1)
[b9/230cca] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_IAA_30M_REP1)
[e7/974aa6] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_IAA_30M_REP1)
[14/7247d2] Submitted process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ (RAP1_UNINDUCED_REP2)
[9b/8bf46d] Submitted process > NFCORE_RNASEQ:RNASEQ:BBMAP_BBSPLIT (1)
[e2/d79519] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (WT_REP1)
[7d/1ade0d] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (RAP1_UNINDUCED_REP1)
[2c/a973b5] Submitted process > NFCORE_RNASEQ:RNASEQ:BBMAP_BBSPLIT (2)
[78/bd4245] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP2)
[c6/dc587a] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP2)
[13/ae9e4b] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP2)
[90/1fb2d5] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_QUANT (WT_REP2)
[60/1adaa4] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (WT_REP1)
[ab/c7180f] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP1)
[12/17a5e5] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP1)
[ff/c74647] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_QUANT (RAP1_IAA_30M_REP1)
[3d/1a73da] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (RAP1_IAA_30M_REP1)
[6a/3c762f] Submitted process > NFCORE_RNASEQ:RNASEQ:BBMAP_BBSPLIT (3)
[f8/705068] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (WT_REP2)
[68/df0d44] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (WT_REP2)
[a3/1cb4d6] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP1)
[04/bf17ff] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP1)
[f4/b16af1] Submitted process > NFCORE_RNASEQ:RNASEQ:BBMAP_BBSPLIT (4)
[60/5d11a8] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (RAP1_IAA_30M_REP1)
[87/d82a10] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (RAP1_IAA_30M_REP1)
[65/d1cf98] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (RAP1_UNINDUCED_REP2)
[b7/f65429] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_QUANT (RAP1_UNINDUCED_REP2)
[b8/5b6e99] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (WT_REP2)
[72/23ae74] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (WT_REP2)
[58/6f62eb] Submitted process > NFCORE_RNASEQ:RNASEQ:BBMAP_BBSPLIT (5)
[5b/5233e6] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (RAP1_UNINDUCED_REP1)
[8d/6b381d] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_QUANT (RAP1_UNINDUCED_REP1)
[ad/a598c3] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (RAP1_IAA_30M_REP1)
[8a/f95c9d] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (RAP1_IAA_30M_REP1)
[56/cc8cb3] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (RAP1_UNINDUCED_REP2)
[b5/492bf7] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (RAP1_UNINDUCED_REP2)
[04/fa9660] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (WT_REP2)
[9a/6adbf3] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (WT_REP2)
[1c/39231d] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (WT_REP2)
[60/d52ef8] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (WT_REP2)
[d1/5f926e] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (WT_REP2)
[28/b88e48] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (WT_REP2)
[66/5afb5e] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)
[b5/c06ce6] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_QUANT (WT_REP1)
[36/c0af01] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (RAP1_UNINDUCED_REP1)
[ca/9f7aea] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (RAP1_UNINDUCED_REP1)
[42/7eea27] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (RAP1_IAA_30M_REP1)
[54/197950] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (RAP1_IAA_30M_REP1)
[ac/e4888d] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (RAP1_IAA_30M_REP1)
[17/2ec801] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (RAP1_IAA_30M_REP1)
[27/20f547] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (RAP1_IAA_30M_REP1)
[82/e410ac] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (RAP1_IAA_30M_REP1)
[87/6089dc] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (RAP1_UNINDUCED_REP2)
[14/554150] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP2)
[83/26a407] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (WT_REP2)
[7c/985003] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (WT_REP2)
[30/b8bdf8] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (WT_REP2)
[81/060168] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (WT_REP2)
[e7/8555b7] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (WT_REP2)
[46/741597] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (WT_REP2)
[f3/61edfd] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (WT_REP2)
[62/dcc432] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (WT_REP2)
[38/362694] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (WT_REP2)
[6b/9f82cd] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (WT_REP2)
[8e/bf4311] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (WT_REP1)
[9d/dabb87] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (WT_REP1)
[36/2c4c22] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_TX2GENE (genome_gfp.gtf)
[90/85cb61] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP1)
[1d/483018] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (RAP1_UNINDUCED_REP1)
[40/35d7e4] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (RAP1_IAA_30M_REP1)
[05/7e3ee6] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (RAP1_IAA_30M_REP1)
[6e/1a53de] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (RAP1_IAA_30M_REP1)
[c8/5bd35b] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (RAP1_IAA_30M_REP1)
[f5/9f11db] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (RAP1_IAA_30M_REP1)
[4d/c4f85a] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (RAP1_IAA_30M_REP1)
[26/64ab08] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (RAP1_IAA_30M_REP1)
[2f/ade923] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (RAP1_IAA_30M_REP1)
[81/d602f8] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (RAP1_IAA_30M_REP1)
[d7/cb2808] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (RAP1_IAA_30M_REP1)
[e8/2e5223] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (RAP1_UNINDUCED_REP2)
[8e/686d16] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP2)
[cc/e9a9c7] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (RAP1_UNINDUCED_REP2)
[d6/229165] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (RAP1_UNINDUCED_REP2)
[21/853146] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (RAP1_UNINDUCED_REP2)
[0e/f67d5c] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (RAP1_UNINDUCED_REP2)
[71/81be66] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (WT_REP2)
[b6/af2600] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (WT_REP2)
[00/09ca0e] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (WT_REP1)
[f2/4bed32] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (WT_REP1)
[fc/36bbec] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (genome_gfp.gtf)
[1a/5c0840] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_TXIMPORT
[31/1e1899] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (RAP1_UNINDUCED_REP1)
[bb/7c0681] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (RAP1_UNINDUCED_REP1)
[a7/feec91] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (RAP1_UNINDUCED_REP1)
[bd/d475c9] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (RAP1_UNINDUCED_REP1)
[6b/b9b2f1] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP1)
[d6/7a9749] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (RAP1_UNINDUCED_REP1)
[6a/c40bf8] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (RAP1_IAA_30M_REP1)
[bf/2e0e8c] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (RAP1_IAA_30M_REP1)
[2b/05a62d] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (RAP1_UNINDUCED_REP2)
[6a/be2b4a] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (RAP1_UNINDUCED_REP2)
[e2/4f0723] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (RAP1_UNINDUCED_REP2)
[d0/ee8d27] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (RAP1_UNINDUCED_REP2)
[9a/b2641a] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (RAP1_UNINDUCED_REP2)
[e1/1b214f] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (RAP1_UNINDUCED_REP2)
[98/4bffbf] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (RAP1_UNINDUCED_REP2)
[89/e1d1af] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (RAP1_UNINDUCED_REP2)
[0c/f99a66] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (RAP1_UNINDUCED_REP2)
[d0/077d60] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (RAP1_UNINDUCED_REP2)
[39/46b97f] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_IAA_30M_REP1)
[59/facbda] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_IAA_30M_REP1)
[a7/a40bcf] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP2)
[0a/4c5d9a] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP1)
[16/88d356] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP2)
[42/ded8b0] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP2)
[bb/1409fa] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP1)
[99/798302] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP2)
[9b/06ff28] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_IAA_30M_REP1)
[26/289bbc] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP1)
[df/6b456a] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP2)
[a0/2507c7] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP1)
[66/502885] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP2)
[e4/7fed86] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP1)
[c4/afc976] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP1)
[35/5ede02] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (WT_REP1)
[4c/2a5659] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (WT_REP1)
[b2/dd0c70] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (WT_REP1)
[cd/4d6f4d] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (WT_REP1)
[ca/85d5db] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (WT_REP1)
[a2/ee3571] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (WT_REP1)
[1c/f1a1a3] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT
[1e/104ec2] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv)
[f3/4637ec] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv)
[a2/f12b27] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv)
[91/a0eae3] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv)
[80/2f32de] Submitted process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_SALMON
[e2/d5955e] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (RAP1_UNINDUCED_REP1)
[3c/503f19] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (RAP1_UNINDUCED_REP1)
[f0/41bcfa] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (RAP1_UNINDUCED_REP1)
[77/456a6d] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (RAP1_UNINDUCED_REP1)
[a3/3b9196] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (RAP1_UNINDUCED_REP1)
[92/a346bc] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (RAP1_UNINDUCED_REP1)
[8a/d1050d] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (RAP1_UNINDUCED_REP1)
[c0/2e749a] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (RAP1_UNINDUCED_REP1)
[ee/5036a5] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (RAP1_UNINDUCED_REP1)
[02/67c235] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (RAP1_UNINDUCED_REP1)
[37/23878c] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP2)
[c9/8b1fc7] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP2)
[f8/e9c078] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (WT_REP1)
[a1/5325a0] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (WT_REP1)
[a5/6343d3] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP2)
[d6/e02e0c] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_IAA_30M_REP1)
[1b/351832] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP2)
[19/6ca4f7] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP1)
[e1/2672da] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP1)
[b1/bb4a51] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_IAA_30M_REP1)
[ed/9127a4] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP2)
[af/23ff00] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP1)
[3d/4b8a7b] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP1)
[57/fef6b1] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_IAA_30M_REP1)
[83/698f30] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP2)
[6b/b2864a] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP2)
[a4/d090e5] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP2)
[a4/ca1e93] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP1)
[27/af2c8e] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (WT_REP1)
[0c/73fc47] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (WT_REP1)
[5f/fbe7f3] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (WT_REP1)
[58/3d88cf] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP1)
[13/8eb525] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (WT_REP1)
[71/d345f6] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (WT_REP1)
[42/018b40] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (WT_REP1)
[8f/77c1ed] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (WT_REP1)
[ef/5c6fa7] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (WT_REP1)
[42/a0d1e7] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv)
[ba/67f839] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv)
[4c/109479] Submitted process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON
[ee/d70396] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv)
[76/aefc75] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv)
[d7/be4af1] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP1)
[db/9489c6] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP1)
[98/aa215a] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (WT_REP1)
[1d/14b280] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (WT_REP1)
[07/b545ae] Submitted process > NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS (1)
[bc/c47f8f] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC (1)
-
[nf-core/rnaseq]
Pipeline completed successfully with skipped sampl(es)
-
-
[nf-core/rnaseq]
Please check MultiQC report: 1/5 samples failed strandedness check.
-
Here, we passed the LaminDB run id to nextflow so that we can query it from within nextflow.
Register outputs#
QC#
multiqc_file = ln.File("rna-seq-results/multiqc/star_salmon/multiqc_report.html")
multiqc_file.save()
How would I register all QC files?
multiqc_results = ln.File.from_dir("rna-seq-results/multiqc/")
ln.save(multiqc_results)
Count matrix#
count_matrix = ln.File("rna-seq-results/salmon/salmon.merged.gene_counts.tsv")
count_matrix.save()
❗ file has more than one suffix (path.suffixes), using only last suffix: '.tsv' - if you want your file format to be recognized, make an issue: https://github.com/laminlabs/lamindb/issues/new
Track Nextflow ID#
Let us look at the nextflow logs:
!nextflow log
TIMESTAMP DURATION RUN NAME STATUS REVISION ID SESSION ID COMMAND
2023-09-20 21:15:54 20m 47s SrkbIyjG3uZcZoCLaSfq OK 5671b65af9 ede90e4c-e1cb-4a61-a41a-1d298fd39cc3 nextflow run nf-core/rnaseq -r 3.11.2 -profile test,docker --outdir rna-seq-results -name SrkbIyjG3uZcZoCLaSfq
Let us add the information about the session ID to our run record:
nextflow_id = getoutput(f"nextflow log | awk '/{run.id}/{{print $8}}'")
run.reference = nextflow_id
run.reference_type = "nextflow_id"
run.save()
Link biological entities#
To make the count matrix queryable by biological entities (genes, experimental metadata, etc.), we can now proceed with: Bulk RNA-seq
Visualize#
View data lineage:
count_matrix.view_flow()
View the database content:
ln.view()
File
| storage_id | key | suffix | accessor | description | version | size | hash | hash_type | transform_id | run_id | initial_version_id | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||
| t8Vx1UX4hPZQxtlEyS7K | xDVZ4rtk | rna-seq-results/salmon/salmon.merged.gene_coun... | .tsv | None | None | None | 3838 | af4b1GaLBBdvP3L8cdb7CQ | md5 | lZgRyrOZ276z6l | SrkbIyjG3uZcZoCLaSfq | None | 2023-09-20 21:36:41 | DzTjkKse |
| p5KWVJ61hOl1egBQtKxa | xDVZ4rtk | rna-seq-results/multiqc/star_salmon/multiqc_re... | .html | None | None | None | 1573394 | 5zCscaerwy8M33H6FX-ueA | md5 | lZgRyrOZ276z6l | SrkbIyjG3uZcZoCLaSfq | None | 2023-09-20 21:36:41 | DzTjkKse |
| cAU5lqgSotatj6WOsfJS | xDVZ4rtk | test-datasets/testdata/GSE110004/SRR6357070_2.... | .fastq.gz | None | None | None | 2232117 | 0SbMZu0Wn2mvLAfaDdc-Ag | md5 | PS57f9enajyu4R | 7QYShc4f4eh6XDVbM5ou | None | 2023-09-20 21:15:38 | DzTjkKse |
| 9qsP3ZksIqaX1Db1GqvL | xDVZ4rtk | test-datasets/testdata/GSE110004/SRR6357074_1.... | .fastq.gz | None | None | None | 2289662 | n2UX-ubh4ChzsZ85nPsKZQ | md5 | PS57f9enajyu4R | 7QYShc4f4eh6XDVbM5ou | None | 2023-09-20 21:15:38 | DzTjkKse |
| KMn5OMbahSJNbvOi61g6 | xDVZ4rtk | test-datasets/testdata/GSE110004/SRR6357071_1.... | .fastq.gz | None | None | None | 2189243 | _RHcJAcS-I8fgAZW_Fm2qw | md5 | PS57f9enajyu4R | 7QYShc4f4eh6XDVbM5ou | None | 2023-09-20 21:15:38 | DzTjkKse |
| Xbl7leRlv68X1Po8ywRz | xDVZ4rtk | test-datasets/testdata/GSE110004/SRR6357075_1.... | .fastq.gz | None | None | None | 2207238 | ak4u6Oo56bYwTqkEtWcJYA | md5 | PS57f9enajyu4R | 7QYShc4f4eh6XDVbM5ou | None | 2023-09-20 21:15:38 | DzTjkKse |
| YsTUcnPhrfA8KOiOYmoq | xDVZ4rtk | test-datasets/testdata/GSE110004/SRR6357070_1.... | .fastq.gz | None | None | None | 2239317 | 0Z88eotAFvpkFFgle5mhoQ | md5 | PS57f9enajyu4R | 7QYShc4f4eh6XDVbM5ou | None | 2023-09-20 21:15:38 | DzTjkKse |
Run
| transform_id | run_at | created_by_id | reference | reference_type | |
|---|---|---|---|---|---|
| id | |||||
| 7QYShc4f4eh6XDVbM5ou | PS57f9enajyu4R | 2023-09-20 21:15:38 | DzTjkKse | https://github.com/nf-core/test-datasets | url |
| SrkbIyjG3uZcZoCLaSfq | lZgRyrOZ276z6l | 2023-09-20 21:15:38 | DzTjkKse | ede90e4c-e1cb-4a61-a41a-1d298fd39cc3 | nextflow_id |
Storage
| root | type | region | updated_at | created_by_id | |
|---|---|---|---|---|---|
| id | |||||
| xDVZ4rtk | /home/runner/work/nextflow-lamin-usecases/next... | local | None | 2023-09-20 21:15:33 | DzTjkKse |
Transform
| name | short_name | version | type | reference | reference_type | initial_version_id | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||
| lZgRyrOZ276z6l | nf-core rnaseq | None | 3.11.2 | pipeline | https://github.com/laminlabs/nextflow-lamin-us... | None | None | 2023-09-20 21:36:41 | DzTjkKse |
| PS57f9enajyu4R | Download | None | None | notebook | None | None | None | 2023-09-20 21:15:38 | DzTjkKse |
User
| handle | name | updated_at | ||
|---|---|---|---|---|
| id | ||||
| DzTjkKse | testuser1 | testuser1@lamin.ai | Test User1 | 2023-09-20 21:15:33 |
Clean up the test instance:
!lamin delete --force nextflow-bulkrna
Show code cell output
💡 deleting instance testuser1/nextflow-bulkrna
✅ deleted instance settings file: /home/runner/.lamin/instance--testuser1--nextflow-bulkrna.env
✅ instance cache deleted
✅ deleted '.lndb' sqlite file
❗ consider manually deleting your stored data: /home/runner/work/nextflow-lamin-usecases/nextflow-lamin-usecases/docs/guide