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Richard Edmunds
1 minute ago#nf-coreHere is my first attempt at writing command for running rnaseq pipeline with mostly default setting but a few variations. Any insights regarding whether or not this is "on track" or wildly incorrect would be heaps appreciated. Thanks!
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nextflow run nf-core-rnaseq_3.12.0/3_12_0/main.nf \
--input C:\Users\redmunds\Desktop\NF-core\Yr2_T1AH_samplesheet.csv ##working with my IT department regarding how to transfer files to/from HPC as this seems better than pointing to desktop folder for sample sheet, etc so I expect this and all other Desktop file paths to change to HPC file paths##
--outdir ~/Yr2_Ahya/T1_trimmed
--multiqc_title "Year 2 A. hyacinthus T=1A and T=1H samples pre- and post-trimming (fastp)" ##not sure if quotes are needed or not?##
--save_merged_fastq
--skip_bbsplit false
--bbsplit_fasta_list C:\Users\redmunds\Desktop\NF-core\Yr2_T1AH_BBSplit.csv
--remove_ribo_rna
--save_non_ribo_reads
--fasta C:\Users\redmnuds\Desktop\Ahya genomes\OIST\ahya.fasta.gz
--gff C:\Users\redmunds\Desktop\Ahya genomes\OIST\ahya.gff.gz
--gtf_group_features "gene" ##GFF annotation uses "gene" not "gene_ID"
--featurecounts_feature_type "gene" ##previous tests with featureCounts used "gene" as feature (not "exon")##
--save_reference
--trimmer 'fastp'
--extra_fastp_args ##(e.g., phred = 30, unqualified = 5%, N = 0) - not sure how to code these options##
--min_trimmed_reads 50
--save_trimmed
--aligner 'star_salmon'
--min_mapped_reads 0.001 ##this lower-than-default number is to keep the handful of samples with low read mapping due to low RNA input##
--save_align_intermeds ##does this save extra .bam files or only those produced by STAR before moving into Salmon for indexing/quantification?##
--skip_markduplicates
--skip_pseudo_alignment
--skip_dupRadar
-profile singularity \
--max_memory '500.GB' \
--max_cpus 50
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marzelwidmer
2 minutes ago#kotlinlangQuestion is the Ktor or KMP Wizard Open Source https://kmp.jetbrains.com/#newProject
https://start.ktor.io/#/settings
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Matt Venn
9 minutes ago#open-source-silicon.devfor lvs, do transistors have to be the right way round? I have this
XM1 osc_a osc_b left_cap VSS sky130_fd_pr__nfet_01v8
for schematic and this XXM1 osc_a VSUBS osc_b left_cap sky130_fd_pr__nfet_01v8_L9BG78
for layout.s
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Maxwell
12 minutes ago#nf-coreHi, I have my nf-core rna-seq pipeline running correctly. However, I want to change my star_salmon_merged_counts.tsv file to include the Ensembl IDs rather than gene symbols in its ouput. The default output is gene symbols which will have duplicate gene names and Ensembl IDs are more specific. Does anyone know how to change this? Thanks for the help!
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Priyaranjan Mudliar
16 minutes ago#Pact FoundationHi !!
I am trying to run a provider verification using ffi lib, but it seems its unable to send the request to (http://localhost:8080/test_weather/generate_weather) verify the message pact :
Code snippet:
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struct VerifierHandle *verifierhandle;
verifierhandle = pactffi_verifier_new_for_application(name, version);
pactffi_verifier_set_provider_info(verifierhandle, name, scheme, host, port, path);
pactffi_verifier_add_provider_transport(verifierhandle, protocol, port, path, scheme);
pactffi_verifier_set_publish_options(verifierhandle, version, NULL, NULL, -1, branch);
pactffi_verifier_add_directory_source(verifierhandle, file_path);
int output = pactffi_verifier_execute(verifierhandle);
pactffi_verifier_shutdown(verifierhandle);
Here are the debug lvl logs attached
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2024-03-17T20:22:21.013948Z DEBUG ThreadId(01) pact_ffi::mock_server::bodies: Path = $
2024-03-17T20:22:21.014020Z DEBUG ThreadId(01) pact_ffi::mock_server::bodies: Configuring a normal object
2024-03-17T20:22:21.014407Z DEBUG ThreadId(01) pact_ffi::mock_server::bodies: Path = $.timestamp
2024-03-17T20:22:21.014430Z DEBUG ThreadId(01) pact_ffi::mock_server::bodies: detected pact:matcher:type, will configure a matcher
2024-03-17T20:22:21.014513Z DEBUG ThreadId(01) pact_ffi::mock_server::bodies: Path = $.weather
2024-03-17T20:22:21.014527Z DEBUG ThreadId(01) pact_ffi::mock_server::bodies: Configuring a normal object
2024-03-17T20:22:21.014541Z DEBUG ThreadId(01) pact_ffi::mock_server::bodies: Path = $.weather.humidity
2024-03-17T20:22:21.014553Z DEBUG ThreadId(01) pact_ffi::mock_server::bodies: detected pact:matcher:type, will configure a matcher
2024-03-17T20:22:21.014575Z DEBUG ThreadId(01) pact_ffi::mock_server::bodies: Path = $.weather.temperature
2024-03-17T20:22:21.014588Z DEBUG ThreadId(01) pact_ffi::mock_server::bodies: detected pact:matcher:type, will configure a matcher
2024-03-17T20:22:21.014614Z DEBUG ThreadId(01) pact_ffi::mock_server::bodies: Path = $.weather.wind_speed_kmh
2024-03-17T20:22:21.014626Z DEBUG ThreadId(01) pact_ffi::mock_server::bodies: detected pact:matcher:type, will configure a matcher
2024-03-17T20:22:21.020918Z DEBUG ThreadId(01) pact_ffi::mock_server::handles: pact_ffi::mock_server::handles::pactffi_pact_handle_write_file FFI function invoked
2024-03-17T20:22:21.021017Z DEBUG ThreadId(01) pact_models::pact: Writing new pact file to "./pacts/animal_service-weather_service.json"
%%% message_pact_SUITE ==> consumer.animal_consume_message: OK
2024-03-17T20:22:21.149207Z DEBUG ThreadId(01) pact_ffi::verifier: pact_ffi::verifier::pactffi_verifier_new_for_application FFI function invoked
2024-03-17T20:22:21.149308Z DEBUG ThreadId(01) pact_ffi::verifier: pact_ffi::verifier::pactffi_verifier_set_provider_info FFI function invoked
2024-03-17T20:22:21.149344Z DEBUG ThreadId(01) pact_ffi::verifier: pact_ffi::verifier::pactffi_verifier_add_provider_transport FFI function invoked
2024-03-17T20:22:21.149391Z DEBUG ThreadId(01) pact_ffi::verifier: pact_ffi::verifier::pactffi_verifier_set_publish_options FFI function invoked
2024-03-17T20:22:21.149421Z DEBUG ThreadId(01) pact_ffi::verifier: pact_ffi::verifier::pactffi_verifier_add_directory_source FFI function invoked
2024-03-17T20:22:21.149453Z DEBUG ThreadId(01) pact_ffi::verifier: pact_ffi::verifier::pactffi_verifier_execute FFI function invoked
2024-03-17T20:22:21.149474Z DEBUG ThreadId(01) pact_ffi::verifier::handle: Pact source to verify = Dir(./pacts)
2024-03-17T20:22:21.153359Z DEBUG ThreadId(01) pact_plugin_driver::catalogue_manager: Updated catalogue entries:
core/content-generator/binary
core/content-generator/json
core/content-matcher/json
core/content-matcher/multipart-form-data
core/content-matcher/text
core/content-matcher/xml
2024-03-17T20:22:21.153423Z DEBUG ThreadId(01) pact_plugin_driver::catalogue_manager: Updated catalogue entries:
core/matcher/v1-equality
core/matcher/v2-max-type
core/matcher/v2-min-type
core/matcher/v2-minmax-type
core/matcher/v2-regex
core/matcher/v2-type
core/matcher/v3-content-type
core/matcher/v3-date
core/matcher/v3-datetime
core/matcher/v3-decimal-type
core/matcher/v3-includes
core/matcher/v3-integer-type
core/matcher/v3-null
core/matcher/v3-number-type
core/matcher/v3-time
core/matcher/v4-array-contains
core/matcher/v4-equals-ignore-order
core/matcher/v4-max-equals-ignore-order
core/matcher/v4-min-equals-ignore-order
core/matcher/v4-minmax-equals-ignore-order
core/matcher/v4-not-empty
core/matcher/v4-semver
2024-03-17T20:22:21.153533Z DEBUG ThreadId(01) pact_verifier: Scanning "./pacts"
2024-03-17T20:22:21.154630Z DEBUG ThreadId(01) verify_interaction{interaction="a weather data message"}: pact_verifier: Executing provider states
2024-03-17T20:22:21.154649Z INFO ThreadId(01) verify_interaction{interaction="a weather data message"}: pact_verifier: Running setup provider state change handler 'weather data for animals' for 'a weather data message'
2024-03-17T20:22:21.154662Z WARN ThreadId(01) verify_interaction{interaction="a weather data message"}: pact_verifier::callback_executors: State Change ignored as there is no state change URL provided for interaction
2024-03-17T20:22:21.154675Z DEBUG ThreadId(01) verify_interaction{interaction="a weather data message"}: pact_verifier: State Change: "ProviderState { name: "weather data for animals", params: {} }" -> Ok({})
2024-03-17T20:22:21.154689Z INFO ThreadId(01) verify_interaction{interaction="a weather data message"}: pact_verifier: Running provider verification for 'a weather data message'
2024-03-17T20:22:21.154696Z DEBUG ThreadId(01) verify_interaction{interaction="a weather data message"}: pact_verifier: Verifying an asynchronous message (single shot)
2024-03-17T20:22:21.154729Z INFO ThreadId(01) verify_interaction{interaction="a weather data message"}: pact_verifier::provider_client: Sending request to provider at <http://localhost:8080/test_weather/generate_weather>
2024-03-17T20:22:21.154737Z DEBUG ThreadId(01) verify_interaction{interaction="a weather data message"}: pact_verifier::provider_client: Provider details = ProviderInfo { name: "weather_service", protocol: "http", host: "localhost", port: Some(8080), path: "/test_weather/generate_weather", transports: [ProviderTransport { transport: "http", port: Some(8080), path: Some("/test_weather/generate_weather"), scheme: None }, ProviderTransport { transport: "message", port: Some(8080), path: Some("/test_weather/generate_weather"), scheme: Some("http") }] }
2024-03-17T20:22:21.154766Z INFO ThreadId(01) verify_interaction{interaction="a weather data message"}: pact_verifier::provider_client: Sending request HTTP Request ( method: POST, path: /, query: None, headers: Some({"Content-Type": ["application/json"]}), body: Present(95 bytes, application/json) )
2024-03-17T20:22:21.154781Z DEBUG ThreadId(01) verify_interaction{interaction="a weather data message"}: pact_verifier::provider_client: body:
{"description":"a weather data message","providerStates":[{"name":"weather data for animals"}]}
2024-03-17T20:22:21.154895Z DEBUG ThreadId(01) verify_interaction{interaction="a weather data message"}: reqwest::connect: starting new connection: <http://localhost:8080/>
2024-03-17T20:22:21.155114Z DEBUG tokio-runtime-worker hyper::client::connect::dns: resolving host="localhost"
2024-03-17T20:22:21.155328Z DEBUG ThreadId(01) verify_interaction{interaction="a weather data message"}: hyper::client::connect::http: connecting to 127.0.0.1:8080
2024-03-17T20:22:21.155535Z DEBUG ThreadId(01) verify_interaction{interaction="a weather data message"}: hyper::client::connect::http: connected to 127.0.0.1:8080
2024-03-17T20:22:21.155860Z DEBUG tokio-runtime-worker hyper::proto::h1::io: flushed 262 bytes
2024-03-17T20:22:26.156256Z INFO ThreadId(01) pact_verifier: Not publishing results as publishing for pact source Dir("./pacts") is not possible or not yet implemented
2024-03-17T20:22:26.156350Z DEBUG ThreadId(01) pact_matching::metrics: 'PACT_DO_NOT_TRACK' environment variable is set, will not send metrics
Verifying a pact between animal_service and weather_service
a weather data message (0s loading, 5s 2ms verification)
Given weather data for animals
Request Failed - error sending request for url (<http://localhost:8080/test_weather/generate_weather>): operation timed out
Failures:
1) Verifying a pact between animal_service and weather_service Given weather data for animals - a weather data message - error sending request for url (<http://localhost:8080/test_weather/generate_weather>): operation timed out
There were 1 pact failures
Also i am able to connect to this particular url via postman, but not via pact ffi. Any clues what could be wrong here?r
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Joe Lin
28 minutes ago#StarRocksHello, I'm having problem to get
hive
catalog working. Below is how I created the catalog
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StarRocks > show catalogs;
+-----------------+----------+------------------------------------------------------------------+
| Catalog | Type | Comment |
+-----------------+----------+------------------------------------------------------------------+
| default_catalog | Internal | An internal catalog contains this cluster's self-managed tables. |
| hive_catalog | Hive | NULL |
+-----------------+----------+------------------------------------------------------------------+
2 rows in set (0.00 sec)
StarRocks > show create catalog hive_catalog;
+--------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Catalog | Create Catalog |
+--------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| hive_catalog | CREATE EXTERNAL CATALOG `hive_catalog`
PROPERTIES ("hive.metastore.type" = "hive",
"hive.metastore.uris" = "<thrift://10.92.31.91:10000>",
"type" = "hive"
) |
+--------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------+
1 row in set (0.00 sec)
But I cannot switch to any database in hive:
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StarRocks > set catalog hive_catalog;
Query OK, 0 rows affected (0.00 sec)
StarRocks > use dwd;
No connection. Trying to reconnect...
Connection id: 9
Current database: *** NONE ***
ERROR 1064 (HY000): Unknown database 'dwd'
StarRocks > use dw;
No connection. Trying to reconnect...
Connection id: 10
Current database: *** NONE ***
ERROR 1064 (HY000): Unknown database 'dw'
Am I missing something?y
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Monte Chan
39 minutes ago#cfmlThis may be a question for Mark and/or the Adobe personnel. Regarding the Adobe CF Builder extension in VS Code, are we allowed to use this Adobe CF Builder extension as a dependency if we were to develop our own VS Code extensions? And if we are allowed to do so, may I ask if there is any documentation on the functions/variables that this Adobe CF Builder extension exposes please?
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Andy Czerwonka
40 minutes ago#FlyteAs an triage adoption spike today, I'm going to attempt to recreate the "Hello World" task and workflow demo via a Scala client that I'll generate against the gRPC interfaces? I'm wondering how much of the Flyte IDL do I need in order to do that? Do I need more that core? e.g. core & service? Do I need
admin
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Dmitriy Tarasevich
42 minutes ago#kotlinlangHas anyone successfully gotten a
ColorDodge
effect to work without strange artifacts. I get this flash of Gray on the shape before the blend mode is applied. There is the code that I am using
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fun Modifier.dodge(
cornerRadius: Dp = 16.dp,
shapeColor: DodgeColor = DodgeColor.GRAY1,
): Modifier {
return composed {
this
.drawWithContent {
drawRoundRect(
cornerRadius = CornerRadius(cornerRadius.toPx()),
color = Color(parseColor(shapeColor.color)),
blendMode = BlendMode.ColorDodge,
)
drawContent()
}
}
}
And an example of what the issue isb
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Carson Miller
about 1 hour ago#nf-coreJust wrapped up in Seattle! We had a lot of people new to Nextflow, and there was a lot of excitement about how easy it is to use nf-core pipelines!
Anybody have specific recommendations that have worked well in the past for introducing people to developing in nf-core?
🎉 2
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