kfukuta/wf-transcriptomes-v202
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Publish isoforms table

Browse Source
This commit is contained in:
Neil Horner 2024-02-09 10:59:01 +00:00
parent 84dbafd1c9
commit fdb938a147
7 changed files with 162 additions and 79 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
CHANGELOG.md
View File

@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- `de_analysis/all_counts_filtered.tsv` to `de_analysis/filtered_transcript_counts_with_genes.tsv` - `de_analysis/all_counts_filtered.tsv` to `de_analysis/filtered_transcript_counts_with_genes.tsv`
- `de_analysis/de_tpm_transcript_counts.tsv` to `de_analysis/unfiltered_tpm_transcript_counts.tsv` - `de_analysis/de_tpm_transcript_counts.tsv` to `de_analysis/unfiltered_tpm_transcript_counts.tsv`
### Added ### Added
- Published isoforms table to output directory.
- Output additional `de_analysis/cpm_gene_counts.tsv` with counts per million gene counts. - Output additional `de_analysis/cpm_gene_counts.tsv` with counts per million gene counts.
- Output additional `de_analysis/unfiltered_transcript_counts_with_genes.tsv` with unfiltered transcript counts with associated gene IDs. - Output additional `de_analysis/unfiltered_transcript_counts_with_genes.tsv` with unfiltered transcript counts with associated gene IDs.
- Add gene name column to the de_analysis counts TSV files. - Add gene name column to the de_analysis counts TSV files.

31
README.md
View File

@ -201,21 +201,22 @@ Output files may be aggregated including information for all samples or provided
| Annotated assembled transcriptome | {{ alias }}_merged_transcriptome.fas | Per sample annotated assembled transcriptome. | per-sample | | Annotated assembled transcriptome | {{ alias }}_merged_transcriptome.fas | Per sample annotated assembled transcriptome. | per-sample |
| Alignment summary statistics | {{ alias }}_read_aln_stats.tsv | Per sample alignment summary statistics. | per-sample | | Alignment summary statistics | {{ alias }}_read_aln_stats.tsv | Per sample alignment summary statistics. | per-sample |
| GFF compare results. | {{ alias }}_gffcompare | All GFF compare output files. | per-sample | | GFF compare results. | {{ alias }}_gffcompare | All GFF compare output files. | per-sample |
| Differential gene expression results | /de_analysis/results_dge.tsv | This is a gene-level result file that describes genes and their probability of showing differential expression between experimental conditions. | aggregated | | Differential gene expression results | de_analysis/results_dge.tsv | This is a gene-level result file that describes genes and their probability of showing differential expression between experimental conditions. | aggregated |
| Differential gene expression report | /de_analysis/results_dge.pdf | Summary report of differential gene expression analysis as a PDF. | aggregated | | Differential gene expression report | de_analysis/results_dge.pdf | Summary report of differential gene expression analysis as a PDF. | aggregated |
| Differential transcript usage gene TSV | /de_analysis/results_dtu_gene.tsv | This is a gene-level result file from DEXSeq that lists annotated genes and their probabilities of differential expression. | aggregated | | Differential transcript usage gene TSV | de_analysis/results_dtu_gene.tsv | This is a gene-level result file from DEXSeq that lists annotated genes and their probabilities of differential expression. | aggregated |
| Differential transcript usage report | /de_analysis/results_dtu.pdf | Summary report of differential transcript usage results as a PDF. | aggregated | | Differential transcript usage report | de_analysis/results_dtu.pdf | Summary report of differential transcript usage results as a PDF. | aggregated |
| Differential transcript usage TSV | /de_analysis/results_dtu_transcript.tsv | This is a transcript-level result file from DEXSeq that lists annotated genes and their probabilities of differential expression. | aggregated | | Differential transcript usage TSV | de_analysis/results_dtu_transcript.tsv | This is a transcript-level result file from DEXSeq that lists annotated genes and their probabilities of differential expression. | aggregated |
| Differential transcript usage stageR TSV | /de_analysis/results_dtu_stageR.tsv | This is the output from StageR and it shows both gene and transcript probabilities of differential expression | aggregated | | Differential transcript usage stageR TSV | de_analysis/results_dtu_stageR.tsv | This is the output from StageR and it shows both gene and transcript probabilities of differential expression | aggregated |
| Differential transcript usage DEXSeq TSV | /de_analysis/results_dexseq.tsv | The complete output from the DEXSeq-analysis, shows both gene and transcript probabilities of differential expression. | aggregated | | Differential transcript usage DEXSeq TSV | de_analysis/results_dexseq.tsv | The complete output from the DEXSeq-analysis, shows both gene and transcript probabilities of differential expression. | aggregated |
| Gene counts | /de_analysis/all_gene_counts.tsv | Raw gene counts created by the Salmon tool, before filtering. | aggregated | | Gene counts | de_analysis/all_gene_counts.tsv | Raw gene counts created by the Salmon tool, before filtering. | aggregated |
| Gene counts per million | /de_analysis/cpm_gene_counts.tsv | This file shows counts per million (CPM) of the raw gene counts to facilitate comparisons across samples. | aggregated | | Gene counts per million | de_analysis/cpm_gene_counts.tsv | This file shows counts per million (CPM) of the raw gene counts to facilitate comparisons across samples. | aggregated |
| Transcript counts | /de_analysis/unfiltered_transcript_counts_with_genes.tsv | Raw transcript counts created by the Salmon tool, before filtering. Includes reference to the associated gene ID. | aggregated | | Transcript counts | de_analysis/unfiltered_transcript_counts_with_genes.tsv | Raw transcript counts created by the Salmon tool, before filtering. Includes reference to the associated gene ID. | aggregated |
| Transcript per million counts | /de_analysis/unfiltered_tpm_transcript_counts.tsv | This file shows transcripts per million (TPM) of the raw counts to facilitate comparisons across samples. | aggregated | | Transcript per million counts | de_analysis/unfiltered_tpm_transcript_counts.tsv | This file shows transcripts per million (TPM) of the raw counts to facilitate comparisons across samples. | aggregated |
| Transcript counts filtered | /de_analysis/filtered_transcript_counts_with_genes.tsv | Filtered transcript counts, used for differential transcript usage analysis. Includes a reference to the associated gene ID. | aggregated | | Transcript counts filtered | de_analysis/filtered_transcript_counts_with_genes.tsv | Filtered transcript counts, used for differential transcript usage analysis. Includes a reference to the associated gene ID. | aggregated |
| Final non redundant transcriptome | /de_analysis/final_non_redundant_transcriptome.fasta | Transcripts that were used for differential expression analysis including novel transcripts with the identifiers used for DE analysis. | aggregated | | Transcript info table | {{ alias }}_transcripts_table.tsv | This file details each isoform that was reconstructed from the input reads. It contains a subset of columns from the .tmap output from [gffcompare](https://ccb.jhu.edu/software/stringtie/gffcompare.shtml) | per-sample |
| Fusion transcript sequences | /jaffal_output_{{ alias }}/jaffa_results.fasta | Fusion transcript sequences output by Jaffa. | per-sample | | Final non redundant transcriptome | de_analysis/final_non_redundant_transcriptome.fasta | Transcripts that were used for differential expression analysis including novel transcripts with the identifiers used for DE analysis. | aggregated |
| Fusion transcript sequence summary file | /jaffal_output_{{ alias }}/jaffa_results.csv | Fusion transcript sequences summary file output by Jaffa. | per-sample | | Fusion transcript sequences | jaffal_output_{{ alias }}/jaffa_results.fasta | Fusion transcript sequences output by Jaffa. | per-sample |
| Fusion transcript sequence summary file | jaffal_output_{{ alias }}/jaffa_results.csv | Fusion transcript sequences summary file output by Jaffa. | per-sample |

68
bin/workflow_glue/make_isoform_table.py Executable file
View File

@ -0,0 +1,68 @@
#!/usr/bin/env python
"""Make report tables and data for plotting."""
from pathlib import Path
import numpy as np
import pandas as pd
from .util import wf_parser # noqa: ABS101
def argparser():
"""Argument parser for entrypoint."""
parser = wf_parser("Prepare report data")
parser.add_argument(
'--sample_id', help="Sample ID", required=True)
parser.add_argument(
'--gffcompare_dir',
help="The gffcompare output directory",
required=False,
type=Path)
return parser
def make_isoform_table(gffcompare_dir, sample_id):
"""Make an isoform summary table."""
try:
tmap_file = next(gffcompare_dir.glob('*.tmap'))
except StopIteration:
raise ValueError("Cannot find .tmap file in {}".format(gffcompare_dir))
dtypes = {
'ref_gene_id': str,
'ref_id': str,
'class_code': str,
'qry_id': str,
'num_exons': np.uint16,
'cov': np.uint32,
'len': np.uint32
}
df = pd.read_csv(
tmap_file, sep='\t+',
index_col=None,
usecols=list(dtypes.keys()),
dtype=dtypes)
if len(df) == 0: # No transcripts. Write a header only result file
df = pd.DataFrame(
columns=list(dtypes.keys()) + ['sample_id', 'parent gene iso num'])
df.to_csv(f'{sample_id}_transcripts_table.tsv', sep='\t', index=False)
else:
df = df.assign(sample_id=sample_id)
# Make a column of number of isoforms in parent gene
gb = df.groupby(['ref_gene_id']).count()
gb.rename(columns={'ref_id': 'num_isoforms'}, inplace=True)
df['parent gene iso num'] = df.apply(
lambda x: gb.loc[(x.ref_gene_id), 'num_isoforms'], axis=1)
# Unclassified transcripts should not be lumped together
df.loc[df.class_code == 'u', 'parent gene iso num'] = None
df.to_csv(f'{sample_id}_transcripts_table.tsv', sep='\t', index=False)
def main(args):
"""Entry point."""
if args.gffcompare_dir:
make_isoform_table(args.gffcompare_dir, args.sample_id)

40
bin/workflow_glue/report.py
View File

@ -59,6 +59,9 @@ def argparser():
parser.add_argument( parser.add_argument(
"--sample_ids", required=True, nargs='+', "--sample_ids", required=True, nargs='+',
help="List of sample ids") help="List of sample ids")
parser.add_argument(
"--isoform_table", required=False, type=Path,
help="Path to directory of TSV files with isoform summaries")
parser.add_argument( parser.add_argument(
"--isoform_table_nrows", required=False, type=int, default=5000, "--isoform_table_nrows", required=False, type=int, default=5000,
help="Maximum rows to display in isoforms table") help="Maximum rows to display in isoforms table")
@ -549,8 +552,6 @@ def gff_compare_plots(report, gffcompare_outdirs, sample_ids):
cover_panel = Tabs(tabs=tabs) cover_panel = Tabs(tabs=tabs)
section.plot(cover_panel) section.plot(cover_panel)
return df_tmap
def pychopper_plots(report, pychop_report): def pychopper_plots(report, pychop_report):
"""Make plots from pychopper output. """Make plots from pychopper output.
@ -648,11 +649,10 @@ def cluster_quality(cluster_qc_dir, report, sample_ids):
section.plot(cover_panel) section.plot(cover_panel)
def transcript_table(report, df_tmaps, max_rows): def transcript_table(report, isoform_table, max_rows):
"""Create searchable table of transcripts. """Create searchable table of transcripts.
:param df_tmaps: pd.DataFrame of all gffcomapre `.tmap` files from all :param isoform_table: path to folder of isoform table files
samples
""" """
section = report.add_section() section = report.add_section()
@ -668,24 +668,11 @@ def transcript_table(report, df_tmaps, max_rows):
`isoform_table_nrows`. It is currently set to `{}` `isoform_table_nrows`. It is currently set to `{}`
'''.format(max_rows)) '''.format(max_rows))
df = df_tmaps.drop( dfs = []
columns=[ for file_ in Path(isoform_table).iterdir():
'FPKM', 'qry_gene_id', 'major_iso_id', 'ref_match_len', 'TPM']) d = pd.read_csv(file_, sep='\t')
dfs.append(d)
if len(df) == 0: df = pd.concat(dfs)
sys.stderr("No transcripts found")
section.markdown("No transcripts found")
return
# Make a column of number of isoforms in parent gene
gb = df.groupby(['ref_gene_id', 'sample_id']).count()
# gb = gb.set_index(['ref_gene_id', 'sample_id'])
gb.rename(columns={'ref_id': 'num_isoforms'}, inplace=True)
df['parent gene iso num'] = df.apply(
lambda x: gb.loc[(x.ref_gene_id, x.sample_id), 'num_isoforms'], axis=1)
# Uncalssified transcritps should not be lumped togetehr
df.loc[df.class_code == 'u', 'parent gene iso num'] = None
# Keep top n rows with most coverage # Keep top n rows with most coverage
df.sort_values('cov', ascending=False, inplace=True) df.sort_values('cov', ascending=False, inplace=True)
@ -934,14 +921,13 @@ def main(args):
report, args.gff_annotation, sample_ids) report, args.gff_annotation, sample_ids)
if args.gffcompare_dir is not None: if args.gffcompare_dir is not None:
df_tmaps = gff_compare_plots( gff_compare_plots(
report, report,
[Path(x) for x in args.gffcompare_dir], [Path(x) for x in args.gffcompare_dir],
sample_ids) sample_ids)
if df_tmaps is not None: if args.isoform_table is not None:
# Skip this section. This needs some work transcript_table(report, args.isoform_table, args.isoform_table_nrows)
transcript_table(report, df_tmaps, args.isoform_table_nrows)
if args.cluster_qc_dirs is not None: if args.cluster_qc_dirs is not None:
cluster_quality(args.cluster_qc_dirs, report, sample_ids) cluster_quality(args.cluster_qc_dirs, report, sample_ids)

31
docs/07_outputs.md
View File

@ -12,18 +12,19 @@ Output files may be aggregated including information for all samples or provided
| Annotated assembled transcriptome | {{ alias }}_merged_transcriptome.fas | Per sample annotated assembled transcriptome. | per-sample | | Annotated assembled transcriptome | {{ alias }}_merged_transcriptome.fas | Per sample annotated assembled transcriptome. | per-sample |
| Alignment summary statistics | {{ alias }}_read_aln_stats.tsv | Per sample alignment summary statistics. | per-sample | | Alignment summary statistics | {{ alias }}_read_aln_stats.tsv | Per sample alignment summary statistics. | per-sample |
| GFF compare results. | {{ alias }}_gffcompare | All GFF compare output files. | per-sample | | GFF compare results. | {{ alias }}_gffcompare | All GFF compare output files. | per-sample |
| Differential gene expression results | /de_analysis/results_dge.tsv | This is a gene-level result file that describes genes and their probability of showing differential expression between experimental conditions. | aggregated | | Differential gene expression results | de_analysis/results_dge.tsv | This is a gene-level result file that describes genes and their probability of showing differential expression between experimental conditions. | aggregated |
| Differential gene expression report | /de_analysis/results_dge.pdf | Summary report of differential gene expression analysis as a PDF. | aggregated | | Differential gene expression report | de_analysis/results_dge.pdf | Summary report of differential gene expression analysis as a PDF. | aggregated |
| Differential transcript usage gene TSV | /de_analysis/results_dtu_gene.tsv | This is a gene-level result file from DEXSeq that lists annotated genes and their probabilities of differential expression. | aggregated | | Differential transcript usage gene TSV | de_analysis/results_dtu_gene.tsv | This is a gene-level result file from DEXSeq that lists annotated genes and their probabilities of differential expression. | aggregated |
| Differential transcript usage report | /de_analysis/results_dtu.pdf | Summary report of differential transcript usage results as a PDF. | aggregated | | Differential transcript usage report | de_analysis/results_dtu.pdf | Summary report of differential transcript usage results as a PDF. | aggregated |
| Differential transcript usage TSV | /de_analysis/results_dtu_transcript.tsv | This is a transcript-level result file from DEXSeq that lists annotated genes and their probabilities of differential expression. | aggregated | | Differential transcript usage TSV | de_analysis/results_dtu_transcript.tsv | This is a transcript-level result file from DEXSeq that lists annotated genes and their probabilities of differential expression. | aggregated |
| Differential transcript usage stageR TSV | /de_analysis/results_dtu_stageR.tsv | This is the output from StageR and it shows both gene and transcript probabilities of differential expression | aggregated | | Differential transcript usage stageR TSV | de_analysis/results_dtu_stageR.tsv | This is the output from StageR and it shows both gene and transcript probabilities of differential expression | aggregated |
| Differential transcript usage DEXSeq TSV | /de_analysis/results_dexseq.tsv | The complete output from the DEXSeq-analysis, shows both gene and transcript probabilities of differential expression. | aggregated | | Differential transcript usage DEXSeq TSV | de_analysis/results_dexseq.tsv | The complete output from the DEXSeq-analysis, shows both gene and transcript probabilities of differential expression. | aggregated |
| Gene counts | /de_analysis/all_gene_counts.tsv | Raw gene counts created by the Salmon tool, before filtering. | aggregated | | Gene counts | de_analysis/all_gene_counts.tsv | Raw gene counts created by the Salmon tool, before filtering. | aggregated |
| Gene counts per million | /de_analysis/cpm_gene_counts.tsv | This file shows counts per million (CPM) of the raw gene counts to facilitate comparisons across samples. | aggregated | | Gene counts per million | de_analysis/cpm_gene_counts.tsv | This file shows counts per million (CPM) of the raw gene counts to facilitate comparisons across samples. | aggregated |
| Transcript counts | /de_analysis/unfiltered_transcript_counts_with_genes.tsv | Raw transcript counts created by the Salmon tool, before filtering. Includes reference to the associated gene ID. | aggregated | | Transcript counts | de_analysis/unfiltered_transcript_counts_with_genes.tsv | Raw transcript counts created by the Salmon tool, before filtering. Includes reference to the associated gene ID. | aggregated |
| Transcript per million counts | /de_analysis/unfiltered_tpm_transcript_counts.tsv | This file shows transcripts per million (TPM) of the raw counts to facilitate comparisons across samples. | aggregated | | Transcript per million counts | de_analysis/unfiltered_tpm_transcript_counts.tsv | This file shows transcripts per million (TPM) of the raw counts to facilitate comparisons across samples. | aggregated |
| Transcript counts filtered | /de_analysis/filtered_transcript_counts_with_genes.tsv | Filtered transcript counts, used for differential transcript usage analysis. Includes a reference to the associated gene ID. | aggregated | | Transcript counts filtered | de_analysis/filtered_transcript_counts_with_genes.tsv | Filtered transcript counts, used for differential transcript usage analysis. Includes a reference to the associated gene ID. | aggregated |
| Final non redundant transcriptome | /de_analysis/final_non_redundant_transcriptome.fasta | Transcripts that were used for differential expression analysis including novel transcripts with the identifiers used for DE analysis. | aggregated | | Transcript info table | {{ alias }}_transcripts_table.tsv | This file details each isoform that was reconstructed from the input reads. It contains a subset of columns from the .tmap output from [gffcompare](https://ccb.jhu.edu/software/stringtie/gffcompare.shtml) | per-sample |
| Fusion transcript sequences | /jaffal_output_{{ alias }}/jaffa_results.fasta | Fusion transcript sequences output by Jaffa. | per-sample | | Final non redundant transcriptome | de_analysis/final_non_redundant_transcriptome.fasta | Transcripts that were used for differential expression analysis including novel transcripts with the identifiers used for DE analysis. | aggregated |
| Fusion transcript sequence summary file | /jaffal_output_{{ alias }}/jaffa_results.csv | Fusion transcript sequences summary file output by Jaffa. | per-sample | | Fusion transcript sequences | jaffal_output_{{ alias }}/jaffa_results.fasta | Fusion transcript sequences output by Jaffa. | per-sample |
| Fusion transcript sequence summary file | jaffal_output_{{ alias }}/jaffa_results.csv | Fusion transcript sequences summary file output by Jaffa. | per-sample |

28
main.nf
View File

@ -303,8 +303,11 @@ process run_gffcompare{
tuple val(sample_id), path(query_annotation) tuple val(sample_id), path(query_annotation)
path ref_annotation path ref_annotation
output: output:
tuple val(sample_id), path("${sample_id}_gffcompare"), emit: gffcmp_dir tuple val(sample_id), path("${sample_id}_gffcompare"),
path ("${sample_id}_annotated.gtf"), emit: gtf, optional: true emit: gffcmp_dir
path ("${sample_id}_annotated.gtf"), emit: gtf
tuple val(sample_id), path("${sample_id}_transcripts_table.tsv"),
emit: isoforms_table
script: script:
def out_dir = "${sample_id}_gffcompare" def out_dir = "${sample_id}_gffcompare"
""" """
@ -320,6 +323,11 @@ process run_gffcompare{
mv *.tmap $out_dir mv *.tmap $out_dir
mv *.refmap $out_dir mv *.refmap $out_dir
cp ${out_dir}/str_merged.annotated.gtf ${sample_id}_annotated.gtf cp ${out_dir}/str_merged.annotated.gtf ${sample_id}_annotated.gtf
# Make an isoform table for report and user output.
workflow-glue make_isoform_table \
--sample_id $sample_id \
--gffcompare_dir "${sample_id}_gffcompare"
""" """
} }
@ -379,7 +387,6 @@ process merge_transcriptomes {
""" """
} }
process makeReport { process makeReport {
label "isoforms" label "isoforms"
@ -398,6 +405,7 @@ process makeReport {
path "gff_annotation/*" path "gff_annotation/*"
path "de_report/*" path "de_report/*"
path "seqkit/*" path "seqkit/*"
path "isoforms_table/*"
output: output:
path("wf-transcriptomes-*.html"), emit: report path("wf-transcriptomes-*.html"), emit: report
// for DE analysis, a `gene_name` column will be added to // for DE analysis, a `gene_name` column will be added to
@ -439,6 +447,11 @@ process makeReport {
else else
OPT_PC_REPORT="--pychop_report pychopper_report/*" OPT_PC_REPORT="--pychop_report pychopper_report/*"
fi fi
if [ -f "isoforms_table/OPTIONAL_FILE" ]; then
OPT_ISO_TABLE=""
else
OPT_ISO_TABLE="--isoform_table isoforms_table"
fi
workflow-glue report --report !{report_name} \ workflow-glue report --report !{report_name} \
--versions !{versions} \ --versions !{versions} \
--params params.json \ --params params.json \
@ -447,6 +460,7 @@ process makeReport {
--sample_ids !{sids} \ --sample_ids !{sids} \
--stats per_read_stats/* \ --stats per_read_stats/* \
${OPT_GFF_ANNOTATION} \ ${OPT_GFF_ANNOTATION} \
${OPT_ISO_TABLE} \
${OPT_GFFCMP_DIR} \ ${OPT_GFFCMP_DIR} \
--isoform_table_nrows !{params.isoform_table_nrows} \ --isoform_table_nrows !{params.isoform_table_nrows} \
${OPT_JAFFAL_CSV} \ ${OPT_JAFFAL_CSV} \
@ -598,6 +612,7 @@ workflow pipeline {
run_gffcompare(merge_gff_bundles.out.gff, ref_annotation) run_gffcompare(merge_gff_bundles.out.gff, ref_annotation)
gff_compare_dir = run_gffcompare.out.gffcmp_dir gff_compare_dir = run_gffcompare.out.gffcmp_dir
gff_compare = run_gffcompare.out.gffcmp_dir.map{ it -> it[1]}.collect() gff_compare = run_gffcompare.out.gffcmp_dir.map{ it -> it[1]}.collect()
isoforms_table = run_gffcompare.out.isoforms_table.map{ it -> it[1]}.collect()
// create per sample gff tuples with gff compare directories // create per sample gff tuples with gff compare directories
gff_tuple = merge_gff_bundles.out.gff gff_tuple = merge_gff_bundles.out.gff
.join(gff_compare_dir) .join(gff_compare_dir)
@ -606,6 +621,7 @@ workflow pipeline {
optional_channel = Channel.fromPath("$projectDir/data/OPTIONAL_FILE") optional_channel = Channel.fromPath("$projectDir/data/OPTIONAL_FILE")
gff_tuple = merge_gff_bundles.out.gff.combine(optional_channel) gff_tuple = merge_gff_bundles.out.gff.combine(optional_channel)
gff_compare = OPTIONAL_FILE gff_compare = OPTIONAL_FILE
isoforms_table = file("$projectDir/data/OPTIONAL_FILE")
} }
// For reference based assembly, there is only one reference // For reference based assembly, there is only one reference
// So map this reference to all sample_ids // So map this reference to all sample_ids
@ -620,6 +636,7 @@ workflow pipeline {
} }
else{ else{
gff_compare = file("$projectDir/data/OPTIONAL_FILE") gff_compare = file("$projectDir/data/OPTIONAL_FILE")
isoforms_table = file("$projectDir/data/OPTIONAL_FILE")
merge_gff = file("$projectDir/data/OPTIONAL_FILE") merge_gff = file("$projectDir/data/OPTIONAL_FILE")
assembly_stats = file("$projectDir/data/OPTIONAL_FILE") assembly_stats = file("$projectDir/data/OPTIONAL_FILE")
use_ref_ann = false use_ref_ann = false
@ -632,7 +649,6 @@ workflow pipeline {
jaffal_out = file("$projectDir/data/OPTIONAL_FILE") jaffal_out = file("$projectDir/data/OPTIONAL_FILE")
} }
if (params.de_analysis){ if (params.de_analysis){
sample_sheet = file(params.sample_sheet, type:"file") sample_sheet = file(params.sample_sheet, type:"file")
if (!params.ref_transcriptome){ if (!params.ref_transcriptome){
@ -670,7 +686,8 @@ workflow pipeline {
gff_compare, gff_compare,
merge_gff, merge_gff,
de_report, de_report,
count_transcripts_file) count_transcripts_file,
isoforms_table)
report = makeReport.out.report report = makeReport.out.report
@ -679,6 +696,7 @@ workflow pipeline {
if (use_ref_ann){ if (use_ref_ann){
results = run_gffcompare.output.gffcmp_dir.concat( results = run_gffcompare.output.gffcmp_dir.concat(
assembly.stats, assembly.stats,
run_gffcompare.out.isoforms_table,
get_transcriptome.out.transcriptome.flatMap(map_sample_ids_cls)) get_transcriptome.out.transcriptome.flatMap(map_sample_ids_cls))
.map {it -> it[1]} .map {it -> it[1]}
.concat(results) .concat(results)

38
output_definition.json
View File

@ -81,7 +81,7 @@
"type": "per-sample" "type": "per-sample"
}, },
"dge-results-tsv": { "dge-results-tsv": {
"filepath": "/de_analysis/results_dge.tsv", "filepath": "de_analysis/results_dge.tsv",
"title": "Differential gene expression results", "title": "Differential gene expression results",
"description": "This is a gene-level result file that describes genes and their probability of showing differential expression between experimental conditions.", "description": "This is a gene-level result file that describes genes and their probability of showing differential expression between experimental conditions.",
"mime-type": "text/tab-separated-values", "mime-type": "text/tab-separated-values",
@ -89,7 +89,7 @@
"type": "aggregated" "type": "aggregated"
}, },
"dge-report-pdf": { "dge-report-pdf": {
"filepath": "/de_analysis/results_dge.pdf", "filepath": "de_analysis/results_dge.pdf",
"title": "Differential gene expression report", "title": "Differential gene expression report",
"description": "Summary report of differential gene expression analysis as a PDF.", "description": "Summary report of differential gene expression analysis as a PDF.",
"mime-type": "application/pdf", "mime-type": "application/pdf",
@ -97,7 +97,7 @@
"type": "aggregated" "type": "aggregated"
}, },
"dtu-gene-tsv": { "dtu-gene-tsv": {
"filepath": "/de_analysis/results_dtu_gene.tsv", "filepath": "de_analysis/results_dtu_gene.tsv",
"title": "Differential transcript usage gene TSV", "title": "Differential transcript usage gene TSV",
"description": "This is a gene-level result file from DEXSeq that lists annotated genes and their probabilities of differential expression.", "description": "This is a gene-level result file from DEXSeq that lists annotated genes and their probabilities of differential expression.",
"mime-type": "text/tab-separated-values", "mime-type": "text/tab-separated-values",
@ -105,7 +105,7 @@
"type": "aggregated" "type": "aggregated"
}, },
"dtu-report-pdf": { "dtu-report-pdf": {
"filepath": "/de_analysis/results_dtu.pdf", "filepath": "de_analysis/results_dtu.pdf",
"title": "Differential transcript usage report", "title": "Differential transcript usage report",
"description": "Summary report of differential transcript usage results as a PDF.", "description": "Summary report of differential transcript usage results as a PDF.",
"mime-type": "application/pdf", "mime-type": "application/pdf",
@ -113,7 +113,7 @@
"type": "aggregated" "type": "aggregated"
}, },
"dtu-transcript": { "dtu-transcript": {
"filepath": "/de_analysis/results_dtu_transcript.tsv", "filepath": "de_analysis/results_dtu_transcript.tsv",
"title": "Differential transcript usage TSV", "title": "Differential transcript usage TSV",
"description": "This is a transcript-level result file from DEXSeq that lists annotated genes and their probabilities of differential expression.", "description": "This is a transcript-level result file from DEXSeq that lists annotated genes and their probabilities of differential expression.",
"mime-type": "text/tab-separated-values", "mime-type": "text/tab-separated-values",
@ -121,7 +121,7 @@
"type": "aggregated" "type": "aggregated"
}, },
"dtu-stageR": { "dtu-stageR": {
"filepath": "/de_analysis/results_dtu_stageR.tsv ", "filepath": "de_analysis/results_dtu_stageR.tsv ",
"title": "Differential transcript usage stageR TSV", "title": "Differential transcript usage stageR TSV",
"description": "This is the output from StageR and it shows both gene and transcript probabilities of differential expression", "description": "This is the output from StageR and it shows both gene and transcript probabilities of differential expression",
"mime-type": "text/tab-separated-values", "mime-type": "text/tab-separated-values",
@ -129,7 +129,7 @@
"type": "aggregated" "type": "aggregated"
}, },
"dexseq": { "dexseq": {
"filepath": "/de_analysis/results_dexseq.tsv", "filepath": "de_analysis/results_dexseq.tsv",
"title": "Differential transcript usage DEXSeq TSV", "title": "Differential transcript usage DEXSeq TSV",
"description": "The complete output from the DEXSeq-analysis, shows both gene and transcript probabilities of differential expression.", "description": "The complete output from the DEXSeq-analysis, shows both gene and transcript probabilities of differential expression.",
"mime-type": "text/tab-separated-values", "mime-type": "text/tab-separated-values",
@ -137,7 +137,7 @@
"type": "aggregated" "type": "aggregated"
}, },
"gene_counts": { "gene_counts": {
"filepath": "/de_analysis/all_gene_counts.tsv", "filepath": "de_analysis/all_gene_counts.tsv",
"title": "Gene counts", "title": "Gene counts",
"description": "Raw gene counts created by the Salmon tool, before filtering.", "description": "Raw gene counts created by the Salmon tool, before filtering.",
"mime-type": "text/tab-separated-values", "mime-type": "text/tab-separated-values",
@ -145,7 +145,7 @@
"type": "aggregated" "type": "aggregated"
}, },
"gene_counts_per_million": { "gene_counts_per_million": {
"filepath": "/de_analysis/cpm_gene_counts.tsv", "filepath": "de_analysis/cpm_gene_counts.tsv",
"title": "Gene counts per million", "title": "Gene counts per million",
"description": "This file shows counts per million (CPM) of the raw gene counts to facilitate comparisons across samples.", "description": "This file shows counts per million (CPM) of the raw gene counts to facilitate comparisons across samples.",
"mime-type": "text/tab-separated-values", "mime-type": "text/tab-separated-values",
@ -153,7 +153,7 @@
"type": "aggregated" "type": "aggregated"
}, },
"transcript_counts": { "transcript_counts": {
"filepath": "/de_analysis/unfiltered_transcript_counts_with_genes.tsv", "filepath": "de_analysis/unfiltered_transcript_counts_with_genes.tsv",
"title": "Transcript counts", "title": "Transcript counts",
"description": "Raw transcript counts created by the Salmon tool, before filtering. Includes reference to the associated gene ID.", "description": "Raw transcript counts created by the Salmon tool, before filtering. Includes reference to the associated gene ID.",
"mime-type": "text/tab-separated-values", "mime-type": "text/tab-separated-values",
@ -161,7 +161,7 @@
"type": "aggregated" "type": "aggregated"
}, },
"tpm_transcript_counts": { "tpm_transcript_counts": {
"filepath": "/de_analysis/unfiltered_tpm_transcript_counts.tsv", "filepath": "de_analysis/unfiltered_tpm_transcript_counts.tsv",
"title": "Transcript per million counts", "title": "Transcript per million counts",
"description": "This file shows transcripts per million (TPM) of the raw counts to facilitate comparisons across samples.", "description": "This file shows transcripts per million (TPM) of the raw counts to facilitate comparisons across samples.",
"mime-type": "text/tab-separated-values", "mime-type": "text/tab-separated-values",
@ -169,15 +169,23 @@
"type": "aggregated" "type": "aggregated"
}, },
"transcipt_counts_filtered": { "transcipt_counts_filtered": {
"filepath": "/de_analysis/filtered_transcript_counts_with_genes.tsv", "filepath": "de_analysis/filtered_transcript_counts_with_genes.tsv",
"title": "Transcript counts filtered", "title": "Transcript counts filtered",
"description": "Filtered transcript counts, used for differential transcript usage analysis. Includes a reference to the associated gene ID.", "description": "Filtered transcript counts, used for differential transcript usage analysis. Includes a reference to the associated gene ID.",
"mime-type": "text/tab-separated-values", "mime-type": "text/tab-separated-values",
"optional": true, "optional": true,
"type": "aggregated" "type": "aggregated"
}, },
"transcripts_table": {
"filepath": "{{ alias }}_transcripts_table.tsv",
"title": "Transcript info table",
"description": "This file details each isoform that was reconstructed from the input reads. It contains a subset of columns from the .tmap output from [gffcompare](https://ccb.jhu.edu/software/stringtie/gffcompare.shtml)",
"mime-type": "text/tab-separated-values",
"optional": true,
"type": "per-sample"
},
"final_non_redundant_transcriptome": { "final_non_redundant_transcriptome": {
"filepath": "/de_analysis/final_non_redundant_transcriptome.fasta", "filepath": "de_analysis/final_non_redundant_transcriptome.fasta",
"title": "Final non redundant transcriptome", "title": "Final non redundant transcriptome",
"description": "Transcripts that were used for differential expression analysis including novel transcripts with the identifiers used for DE analysis.", "description": "Transcripts that were used for differential expression analysis including novel transcripts with the identifiers used for DE analysis.",
"mime-type": "text/x-fasta", "mime-type": "text/x-fasta",
@ -185,7 +193,7 @@
"type": "aggregated" "type": "aggregated"
}, },
"jaffa_fasta": { "jaffa_fasta": {
"filepath": "/jaffal_output_{{ alias }}/jaffa_results.fasta", "filepath": "jaffal_output_{{ alias }}/jaffa_results.fasta",
"title": "Fusion transcript sequences", "title": "Fusion transcript sequences",
"description": "Fusion transcript sequences output by Jaffa.", "description": "Fusion transcript sequences output by Jaffa.",
"mime-type": "text/x-fasta", "mime-type": "text/x-fasta",
@ -193,7 +201,7 @@
"type": "per-sample" "type": "per-sample"
}, },
"jaffa_results": { "jaffa_results": {
"filepath": "/jaffal_output_{{ alias }}/jaffa_results.csv", "filepath": "jaffal_output_{{ alias }}/jaffa_results.csv",
"title": "Fusion transcript sequence summary file", "title": "Fusion transcript sequence summary file",
"description": "Fusion transcript sequences summary file output by Jaffa.", "description": "Fusion transcript sequences summary file output by Jaffa.",
"mime-type": "text/csv", "mime-type": "text/csv",