Skip to content
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

Run qc on samples #102

Merged
merged 3 commits into from
Dec 6, 2016
Merged

Run qc on samples #102

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
14a7920
Realign all RNA BAMs together
ihodes Dec 1, 2016
1d64d0c
Run FASTQC on a per-sample basis
ihodes Dec 6, 2016
65ceed4
Open Option more locally
ihodes Dec 6, 2016
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
14 changes: 4 additions & 10 deletions src/lib/extended_edsl.ml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -60,23 +60,19 @@ module Apply_functions (B : Semantics) = struct
in
fwd email

let fastqc_email ~normal ~tumor ?rna email_options =
let fastqc_email ~fastqcs email_options =
let open The_pass.Transformation in
let email =
(B.fastqc_email
~normal:(bwd normal)
~tumor:(bwd tumor)
?rna:(Option.map rna bwd)
~fastqcs:(List.map ~f:(fun (name, f) -> (name, bwd f)) fastqcs)
email_options)
in
fwd email

let report
?igv_url_server_prefix
~vcfs
~fastqc_normal
~fastqc_tumor
?fastqc_rna
~fastqcs
~normal_bam
~normal_bam_flagstat
~tumor_bam
Expand All @@ -97,9 +93,7 @@ module Apply_functions (B : Semantics) = struct
let open The_pass.Transformation in
fwd (B.report meta
~vcfs:(List.map ~f:(fun (k, v) -> k, bwd v) vcfs)
~fastqc_normal:(bwd fastqc_normal)
~fastqc_tumor:(bwd fastqc_tumor)
?fastqc_rna:(Option.map fastqc_rna bwd)
~fastqcs:(List.map ~f:(fun (name, f) -> (name, bwd f)) fastqcs)
~normal_bam:(bwd normal_bam)
~normal_bam_flagstat:(bwd normal_bam_flagstat)
~tumor_bam:(bwd tumor_bam)
Expand Down
57 changes: 16 additions & 41 deletions src/lib/final_report.ml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,9 +27,7 @@ module type Semantics = sig
val report :
?igv_url_server_prefix: string ->
vcfs:(string * [ `Vcf ] repr) list ->
fastqc_normal: [ `Fastqc ] repr ->
fastqc_tumor: [ `Fastqc ] repr ->
?fastqc_rna: [ `Fastqc ] repr ->
fastqcs:(string * [ `Fastqc ] repr) list ->
normal_bam: [ `Bam ] repr ->
normal_bam_flagstat: [ `Flagstat ] repr ->
tumor_bam: [ `Bam ] repr ->
Expand Down Expand Up @@ -57,9 +55,7 @@ module To_json = struct
let report
?igv_url_server_prefix
~vcfs
~fastqc_normal
~fastqc_tumor
?fastqc_rna
~fastqcs
~normal_bam
~normal_bam_flagstat
~tumor_bam
Expand All @@ -86,9 +82,9 @@ module To_json = struct
"metadata", `Assoc (List.map metadata ~f:(fun (k, v) -> k, `String v));
]
@ List.map vcfs ~f:(fun (k, v) -> k, v ~var_count)
@ List.map fastqcs
~f:(fun (name, f) -> sprintf "%s-fastqc" name, f ~var_count)
@ [
"qc-normal", fastqc_normal ~var_count;
"qc-tumor", fastqc_tumor ~var_count;
"normal-bam", normal_bam ~var_count;
"tumor-bam", tumor_bam ~var_count;
"normal-bam-flagstat", normal_bam_flagstat ~var_count;
Expand All @@ -98,7 +94,6 @@ module To_json = struct
@ opt "optitype-tumor" optitype_tumor
@ opt "optitype-rna" optitype_rna
@ opt "rna-bam" rna_bam
@ opt "rna-fastqc" fastqc_rna
@ opt "rna-bam-flagstat" rna_bam_flagstat
@ opt "vaxrank" vaxrank
@ opt "topiary" topiary
Expand Down Expand Up @@ -139,9 +134,7 @@ module To_dot = struct
let report
?igv_url_server_prefix
~vcfs
~fastqc_normal
~fastqc_tumor
?fastqc_rna
~fastqcs
~normal_bam
~normal_bam_flagstat
~tumor_bam
Expand All @@ -166,9 +159,9 @@ module To_dot = struct
["run-name", string meta;]
@ List.map vcfs ~f:(fun (k, v) ->
k, v ~var_count)
@ List.map fastqcs
~f:(fun (name, f) -> sprintf "%s-fastqc" name, f ~var_count)
@ [
"qc-normal", fastqc_normal ~var_count;
"qc-tumor", fastqc_tumor ~var_count;
"normal-bam", normal_bam ~var_count;
"tumor-bam", tumor_bam ~var_count;
"normal-bam-flagstat", normal_bam_flagstat ~var_count;
Expand All @@ -178,7 +171,6 @@ module To_dot = struct
@ opt "optitype-tumor" optitype_tumor
@ opt "optitype-rna" optitype_rna
@ opt "rna-bam" rna_bam
@ opt "rna-fastqc" fastqc_rna
@ opt "rna-bam-flagstat" rna_bam_flagstat
@ opt "vaxrank" vaxrank
@ opt "topiary" topiary
Expand Down Expand Up @@ -266,9 +258,7 @@ module To_workflow
let report
?igv_url_server_prefix
~vcfs
~fastqc_normal
~fastqc_tumor
?fastqc_rna
~fastqcs
~normal_bam
~normal_bam_flagstat
~tumor_bam
Expand Down Expand Up @@ -341,9 +331,8 @@ module To_workflow
Option.value_map o ~default:[] ~f:(fun v -> [ f v |> depends_on ]) in
depends_on igv_dot_xml
:: List.map vcfs ~f:(fun (_, v) -> get_vcf v |> depends_on)
@ List.map fastqcs ~f:(fun (_, f) -> get_fastqc_result f |> depends_on)
@ [
get_fastqc_result fastqc_normal |> depends_on;
get_fastqc_result fastqc_tumor |> depends_on;
get_bam normal_bam |> depends_on;
get_bam tumor_bam |> depends_on;
get_flagstat_result tumor_bam_flagstat |> depends_on;
Expand All @@ -353,7 +342,6 @@ module To_workflow
@ opt optitype_tumor get_optitype_result
@ opt optitype_rna get_optitype_result
@ opt rna_bam get_bam
@ opt fastqc_rna get_fastqc_result
@ opt vaxrank get_vaxrank_result
@ opt rna_bam_flagstat get_flagstat_result
@ opt topiary get_topiary_result
Expand Down Expand Up @@ -475,25 +463,14 @@ module To_workflow
in
let qc_section =
let open Option in
let n = get_fastqc_result fastqc_normal in
let t = get_fastqc_result fastqc_tumor in
let r = fastqc_rna >>= fun r -> return (get_fastqc_result r) in
let items =
List.filter_map [
(List.nth n#product#paths 0, "FastQC Normal : Read 1");
(List.nth n#product#paths 1, "FastQC Normal : Read 2");
(List.nth t#product#paths 0, "FastQC Tumor : Read 1");
(List.nth t#product#paths 1, "FastQC Tumor : Read 2");
((r >>= fun r -> List.nth r#product#paths 0), "FastQC RNA : Read 1");
((r >>= fun r -> List.nth r#product#paths 1), "FastQC RNA : Read 2");
]
~f:(function
| None, _ -> None
| Some p, title ->
Some (list_item title p))
List.concat_map fastqcs
~f:(fun (name, f) ->
let f = get_fastqc_result f in
List.mapi f#product#paths ~f:(fun i p ->
let title = sprintf "%s : Read %d" name i in
list_item title p))
in
let _, json =
saved_paths ~json_of_dirname:true (List.nth_exn n#product#paths 0) in
let inline_code name cmd =
let id = Digest.(string name |> to_hex) in
let button = "☟" in
Expand All @@ -514,10 +491,8 @@ module To_workflow
`String (
sprintf {html|<h2>Dataset QC</h2><ul>
%s
<li>FastqQC Pipeline: %s</li>
|html}
(String.concat ~sep:"\n" items)
(relative_link ~href:json "JSON"));
(String.concat ~sep:"\n" items));
]
@ inline_code "Normal Bam Flagstat"
(cat_flatstat normal_bam_flagstat)
Expand Down
Loading