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dispatcher + ofs update
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@tahirdme
tahirdme committed Oct 1, 2024
1 parent c3805f5 commit 0f3290b
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Showing 6 changed files with 53 additions and 53 deletions.
2 changes: 1 addition & 1 deletion .latch/Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
# DO NOT CHANGE
from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.1.2

workdir /tmp/docker-build/work/

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2 changes: 1 addition & 1 deletion .latch/config
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@@ -1 +1 @@
{"latch_version": "2.52.1", "base_image": "812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0", "date": "2024-09-12T12:57:15.404807"}
{"latch_version": "2.52.1", "base_image": "812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.1.2", "date": "2024-09-12T12:57:15.404807"}
1 change: 1 addition & 0 deletions latch_metadata/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@
Section(
"Input",
Params("input"),
Text("Samplesheet expects 'control' column to be filled for all non-control samples."),
Spoiler(
"Optional",
Params("use_control"),
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91 changes: 45 additions & 46 deletions latch_metadata/parameters.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
import typing
from dataclasses import dataclass
from enum import Enum
from typing import List, Optional

from latch.types.directory import LatchDir, LatchOutputDir
from latch.types.file import LatchFile
Expand All @@ -13,7 +13,7 @@ class SampleSheet:
replicate: int
fastq_1: LatchFile
fastq_2: LatchFile
control: str
control: Optional[str]


class Reference(Enum):
Expand All @@ -23,7 +23,7 @@ class Reference(Enum):

generated_parameters = {
"input": NextflowParameter(
type=typing.List[SampleSheet],
type=List[SampleSheet],
display_name="Input",
description="Information about the samples in the experiment",
section_title=None,
Expand All @@ -38,7 +38,7 @@ class Reference(Enum):
description="The output directory where the results will be saved. You have to use absolute paths to store on Cloud infrastructure.",
),
"multiqc_title": NextflowParameter(
type=typing.Optional[str],
type=Optional[str],
default=None,
section_title=None,
display_name="MultiQC Title",
Expand All @@ -64,9 +64,8 @@ class Reference(Enum):
description="Choose Reference Genome",
),
"latch_genome": NextflowParameter(
type=typing.Optional[Reference],
type=Optional[Reference],
default=None,
section_title="Reference genome options",
display_name="Genome",
description="Name of the Latch Verfied Reference Genome",
),
Expand Down Expand Up @@ -99,7 +98,7 @@ class Reference(Enum):
description="Save alignment intermediates to the output directory (WARNING: can be very large)",
),
"email": NextflowParameter(
type=typing.Optional[str],
type=Optional[str],
default=None,
section_title=None,
display_name="Email",
Expand All @@ -113,63 +112,63 @@ class Reference(Enum):
description="Output calculated scale factors from pipeline",
),
"genome": NextflowParameter(
type=typing.Optional[str],
type=Optional[str],
default=None,
section_title=None,
display_name="Genome",
description="Name of iGenomes reference.",
),
"bowtie2": NextflowParameter(
type=typing.Optional[LatchDir],
type=Optional[LatchDir],
default=None,
section_title=None,
display_name="Bowtie2",
description="Path to bowtie2 index",
),
"gtf": NextflowParameter(
type=typing.Optional[LatchFile],
type=Optional[LatchFile],
default=None,
section_title=None,
display_name="GTF",
description="Path to GTF annotation file",
),
"gene_bed": NextflowParameter(
type=typing.Optional[LatchFile],
type=Optional[LatchFile],
default=None,
section_title=None,
display_name="Gene Bed",
description="Path to gene BED file",
),
"blacklist": NextflowParameter(
type=typing.Optional[LatchFile],
type=Optional[LatchFile],
default=None,
section_title=None,
display_name="Blacklist",
description="Path to genome blacklist",
),
"spikein_genome": NextflowParameter(
type=typing.Optional[str],
type=Optional[str],
default="K12-MG1655",
section_title=None,
display_name="Spikein Genome",
description="Name of the iGenome reference for the spike-in genome, defaulting to E. coli K12, for yeast set to R64-1-1, for fruit fly BDGP6",
),
"spikein_bowtie2": NextflowParameter(
type=typing.Optional[LatchFile],
type=Optional[LatchFile],
default=None,
section_title=None,
display_name="Spikein Bowtie2",
description="Path to spike-in bowtie2 index",
),
"spikein_fasta": NextflowParameter(
type=typing.Optional[LatchFile],
type=Optional[LatchFile],
default=None,
section_title=None,
display_name="Spikein Fasta",
description="Path to spike-in fasta",
),
"fasta": NextflowParameter(
type=typing.Optional[LatchFile],
type=Optional[LatchFile],
default=None,
section_title=None,
display_name="Fasta",
Expand Down Expand Up @@ -288,42 +287,42 @@ class Reference(Enum):
description="Skips multiqc",
),
"clip_r1": NextflowParameter(
type=typing.Optional[int],
type=Optional[int],
default=0,
section_title=None,
display_name="Clip R1",
description="Instructs Trim Galore to remove bp from the 5' end of read 1 (or single-end reads).",
),
"clip_r2": NextflowParameter(
type=typing.Optional[int],
type=Optional[int],
default=0,
section_title=None,
display_name="Clip R2",
description="Instructs Trim Galore to remove bp from the 5' end of read 2 (paired-end reads only).",
),
"three_prime_clip_r1": NextflowParameter(
type=typing.Optional[int],
type=Optional[int],
default=0,
section_title=None,
display_name="Three Prime Clip R1",
description="Instructs Trim Galore to remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed.",
),
"three_prime_clip_r2": NextflowParameter(
type=typing.Optional[int],
type=Optional[int],
default=0,
section_title=None,
display_name="Three Prime Clip R2",
description="Instructs Trim Galore to remove bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed.",
),
"trim_nextseq": NextflowParameter(
type=typing.Optional[int],
type=Optional[int],
default=0,
section_title=None,
display_name="Trim NextSeq",
description="Instructs Trim Galore to apply the --nextseq=X option, to trim based on quality after removing poly-G tails.",
),
"minimum_alignment_q_score": NextflowParameter(
type=typing.Optional[int],
type=Optional[int],
default=20,
section_title=None,
display_name="Minimum Alignment Q Score",
Expand All @@ -349,7 +348,7 @@ class Reference(Enum):
],
),
"mito_name": NextflowParameter(
type=typing.Optional[str],
type=Optional[str],
default=None,
section_title=None,
display_name="Mito Name",
Expand Down Expand Up @@ -377,22 +376,22 @@ class Reference(Enum):
description="Use --end-to-end mode of Bowtie2 during alignment",
),
"normalisation_mode": NextflowParameter(
type=typing.Optional[str],
type=Optional[str],
default="Spikein",
section_title=None,
display_name="Normalisation Mode",
appearance_type=Multiselect(["Spikein", "RPKM", "CPM", "BPM", "None"], allow_custom=False),
description='Sets the target read normalisation mode. Options are: ["Spikein", "RPKM", "CPM", "BPM", "None" ]',
),
"normalisation_binsize": NextflowParameter(
type=typing.Optional[int],
type=Optional[int],
default=50,
section_title=None,
display_name="Normalisation Binsize",
description='If normalisation option is one of "RPKM", "CPM", "BPM" - then the binsize that the reads count is calculated on is used.',
),
"peakcaller": NextflowParameter(
type=typing.Optional[str],
type=Optional[str],
default="seacr",
section_title=None,
display_name="Peakcaller",
Expand All @@ -414,51 +413,51 @@ class Reference(Enum):
description="Specifies whether to extend paired-end fragments between the read mates when calculating coverage tracks",
),
"igg_scale_factor": NextflowParameter(
type=typing.Optional[float],
type=Optional[float],
default=0.5,
section_title=None,
display_name="IGG Scale Factor",
description="Specifies whether the background control is scaled prior to being used to normalise peaks.",
),
"seacr_peak_threshold": NextflowParameter(
type=typing.Optional[float],
type=Optional[float],
default=0.05,
section_title=None,
display_name="SEACR Peak Threshold",
description="SEACR specifies returns the top n fraction (between 0 and 1) of peaks based on total signal within peaks. This is only used if there are no controls included with the samples and if `--use_control` is `false`",
),
"seacr_norm": NextflowParameter(
type=typing.Optional[str],
type=Optional[str],
default="non",
section_title=None,
appearance_type=Multiselect(["non", "norm"], allow_custom=False),
display_name="SEACR Norm",
description="SEACR normalization.",
),
"seacr_stringent": NextflowParameter(
type=typing.Optional[str],
type=Optional[str],
default="stringent",
section_title=None,
appearance_type=Multiselect(["stringent", "relaxed"], allow_custom=False),
display_name="SEACR Stringency",
description="SEACR stringency.",
),
"macs2_qvalue": NextflowParameter(
type=typing.Optional[float],
type=Optional[float],
default=0.01,
section_title=None,
display_name="MACS2 Q-value",
description="Q-value threshold for MACS2 peak caller.",
),
"macs2_pvalue": NextflowParameter(
type=typing.Optional[float],
type=Optional[float],
default=None,
section_title=None,
display_name="MACS2 P-value",
description="P-value threshold for macs2 peak caller. If set it will override the q-value.",
),
"macs_gsize": NextflowParameter(
type=typing.Optional[float],
type=Optional[float],
default=2700000000.0,
section_title=None,
display_name="MACS Gsize",
Expand All @@ -472,22 +471,22 @@ class Reference(Enum):
description="Determines whether MACS2 broad or narrow peak mode is used for the peak caller",
),
"macs2_broad_cutoff": NextflowParameter(
type=typing.Optional[float],
type=Optional[float],
default=0.1,
section_title=None,
display_name="MACS2 Broad Cutoff",
description="MACS2 broad cutoff parameter",
),
"consensus_peak_mode": NextflowParameter(
type=typing.Optional[str],
type=Optional[str],
default="group",
section_title=None,
display_name="Consensus Peak Mode",
appearance_type=Multiselect(["group", "all"], allow_custom=False),
description="Specifies what samples to group together for consensus peaks. Options are [group, all]",
),
"replicate_threshold": NextflowParameter(
type=typing.Optional[float],
type=Optional[float],
default=1.0,
section_title=None,
display_name="Replicate Threshold",
Expand All @@ -501,49 +500,49 @@ class Reference(Enum):
description="Show gene names instead of symbols in IGV browser sessions",
),
"dt_qc_bam_binsize": NextflowParameter(
type=typing.Optional[int],
type=Optional[int],
default=500,
section_title=None,
display_name="DT QC BAM Binsize",
description="Deeptools multiBamSummary bam bin size",
),
"dt_qc_corr_method": NextflowParameter(
type=typing.Optional[str],
type=Optional[str],
default="pearson",
section_title=None,
display_name="DT QC Corr Method",
description="Deeptools Correlation Plot statistical calculation method",
),
"dt_heatmap_gene_beforelen": NextflowParameter(
type=typing.Optional[int],
type=Optional[int],
default=3000,
section_title=None,
display_name="DT Heatmap Gene Beforelen",
description="Deeptools heatmap gene plot before length (bases)",
),
"dt_heatmap_gene_bodylen": NextflowParameter(
type=typing.Optional[int],
type=Optional[int],
default=5000,
section_title=None,
display_name="DT Heatmap Gene Bodylen",
description="Deeptools heatmap gene plot body length (bases)",
),
"dt_heatmap_gene_afterlen": NextflowParameter(
type=typing.Optional[int],
type=Optional[int],
default=3000,
section_title=None,
display_name="DT Heatmap Gene Afterlen",
description="Deeptools heatmap gene plot after length (bases)",
),
"dt_heatmap_peak_beforelen": NextflowParameter(
type=typing.Optional[int],
type=Optional[int],
default=3000,
section_title=None,
display_name="DT Heatmap Peak Beforelen",
description="Deeptools heatmap peak plot before length (bases)",
),
"dt_heatmap_peak_afterlen": NextflowParameter(
type=typing.Optional[int],
type=Optional[int],
default=3000,
section_title=None,
display_name="DT Heatmap Peak Afterlen",
Expand All @@ -557,14 +556,14 @@ class Reference(Enum):
description="Flag for whether to generate a heatmap for all samples together",
),
"min_frip_overlap": NextflowParameter(
type=typing.Optional[float],
type=Optional[float],
default=0.2,
section_title=None,
display_name="Min FRiP Overlap",
description="Minimum fragment overlap for FriP score",
),
"min_peak_overlap": NextflowParameter(
type=typing.Optional[float],
type=Optional[float],
default=0.2,
section_title=None,
display_name="Min Peak Overlap",
Expand All @@ -585,7 +584,7 @@ class Reference(Enum):
description="Pull Docker container.",
),
"multiqc_methods_description": NextflowParameter(
type=typing.Optional[str],
type=Optional[str],
default=None,
section_title=None,
display_name="MultiQC Methods Description",
Expand Down
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