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dkj/10XQC 0

A system for monitoring the quality of 10X single cell data

dkj/artic-ncov2019 0

ARTIC nanopore protocol for nCoV2019 novel coronavirus

dkj/assembly-stats 0

Get assembly statistics from FASTA and FASTQ files

dkj/bambi 0

A set of programs to manipulate SAM/BAM/CRAM files, using HTSLIB

dkj/BamSeqChksumJava 0

Prototype implementation of BAM checksumming in Java

dkj/baton 0

iRODS client programs and API

dkj/bcftools 0

This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib

dkj/bcviz 0

JavaScript visualisation for bamcheck file format

dkj/BEETL 0

BEETL

pull request commentwtsi-npg/npg_qc

falback for max_negative_control_filtered_read_count

Wondering if this is too pessimistic. Do we see 0 aligned reads out of artic QC?

mgcam

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PR opened wtsi-npg/npg_conda

fix jansson 2.10 recipe path (purge incorrect 2.1.0)

Follow up to #208 (not sure why git mv didn't work as I thought - sorry!)

+0 -72

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Keith James

commit sha 870985654bf12f75f3487448eab28afe23657102

Update the default build image for iRODS 4.1

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dkj

commit sha 95bb0010095c89a32c4195c519bb97f1fec1eddf

Merge pull request #192 from kjsanger/feature/update-irods-build-image Update the default build image for iRODS 4.1

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Keith James

commit sha 29d7d696c15d639939dc65349a596b785db934d9

Merge pull request #208 from dkj/jansson210path fix jansson 2.10 recipe path

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David K. Jackson

commit sha 0c4c8b77071be7c12b3ef00c0a66e979e32c4c6c

fix jansson 2.10 recipe path (purge incorrect 2.1.0)

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Marina Gourtovaia

commit sha 86593273fcc6b1f37d69eb469545c32bb12c58e3

mlwh loader extension for ampliconstats data

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dkj

commit sha 99ca5cdd3b766453e7c235dfc1711f0c3f6d168f

Merge pull request #170 from mgcam/loader4ampliconstats mlwh loader extension for ampliconstats

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PR merged wtsi-npg/npg_ml_warehouse

mlwh loader extension for ampliconstats

Depends on https://github.com/wtsi-npg/ml_warehouse/pull/155 To be tested against the dev db

+385 -134

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mgcam

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Marina Gourtovaia

commit sha 10275df59fd3e614f18149e13fdc9967a19f87bf

retrieval and loading of heron artic data is refactored to make the code more generic and flexible

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dkj

commit sha 370c212cfe469ebd52e6341daa402a27f22fd2de

Merge pull request #169 from mgcam/loader4pp_refactor refactoring of retrieval and loading of heron artic data

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Keith James

commit sha 870985654bf12f75f3487448eab28afe23657102

Update the default build image for iRODS 4.1

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dkj

commit sha 95bb0010095c89a32c4195c519bb97f1fec1eddf

Merge pull request #192 from kjsanger/feature/update-irods-build-image Update the default build image for iRODS 4.1

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PR opened wtsi-npg/npg_conda

fix jansson 2.10 recipe path
+72 -0

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Keith James

commit sha 0595775e8409ee532b820e076715b1e0007d4327

Bugfix: apply the RENCI patch "imeta qu no longer ignores -z option"

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dkj

commit sha 6d504da18ffdb7daeaa8bb861680647a9a59b1cd

Merge pull request #206 from kjsanger/bugfix/imeta-zone-cli Add the RENCI fix for imeta ignoring the -z argument

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PR merged wtsi-npg/npg_conda

Add the RENCI fix for imeta ignoring the -z argument bug

Add the RENCI fix for imeta ignoring the -z argument

Requires #205

+132 -152

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kjsanger

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Keith James

commit sha 0f35cabe42ec5cafb2f398c312a4562dea511357

Enable a clean iRODS build with fewer dependencies Add a dependency on our avrocpp build (built with boost 1.73.0 support to remove other dependencies). Add a dependency on our boost 1.73.0 build (built without Python support to remove other dependencies). Remove the boost-cpp (conda-forge) dependency. Remove the krb runtime dependency to avoid conflicts (we don't support Kerberos clients). Remove the gzip build dependency (not needed). Lint and sort the build recipe for maintenance. Fix git submodule init for iRODS to be done in the correct directory. Lint and organise the build script for maintenance/clarity. Remove legacy functions from build.sh

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dkj

commit sha 0d8d3ae9239d2f1180f4d493c6ee8ab324cc6774

Merge pull request #205 from kjsanger/bugfix/clean-irods-4.2.7 Enable a clean iRODS build with fewer dependencies

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PR merged wtsi-npg/npg_conda

Reviewers
Enable a clean iRODS build with fewer dependencies bug

Add a dependency on our avrocpp build (built with boost 1.73.0 support to remove other dependencies).

Add a dependency on our boost 1.73.0 build (built without Python support to remove other dependencies). Remove the boost-cpp (conda-forge) dependency.

Remove the krb runtime dependency to avoid conflicts (we don't support Kerberos clients).

Remove the gzip build dependency (not needed).

Lint and sort the build recipe for maintenance.

Fix git submodule init for iRODS to be done in the correct directory.

Lint and organise the build script for maintenance/clarity.

Remove legacy functions from build.sh

+93 -152

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kjsanger

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PR merged wtsi-npg/npg_conda

Ensure local version part matches version candidates bug

Reconcile differences between PEP440 (the API being used here) and Conda, which is mostly, but not always compatible with PEP440 and has a different implementation.

+233 -9

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kjsanger

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PR merged wtsi-npg/npg_conda

Reduce avrocpp dependencies bug

Remove specific dependency boost-cpp and use our boost 1.73.0, which is built without Python support. This prevents many other packages from conda-forge being depended upon, including py-boost, python, numpy.

Remove non-Linux clauses from avrocpp recipe.

Move avrocpp from red-recipes to recipes as it no longer depends on conda-forge.

+93 -96

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kjsanger

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PR merged wtsi-npg/npg_conda

Append rather than add build channels enhancement

Append rather than add build channels (e.g. conda-forge) so that their precedence is lower than defaults.

+1 -1

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kjsanger

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PR merged wtsi-npg/npg_conda

Add boost 1.73.0 enhancement
+99 -0

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kjsanger

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Keith James

commit sha 1cdfae776055a8f7c41c2b6a2c183f1c5d8de130

Bugfix: ensure local version part matches version candidates Reconcile differences between PEP440 (the API being used here) and Conda, which is mostly, but not always compatible with PEP440 and has a different implementation.

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Keith James

commit sha 2b778deb866f0c070d45338d423061dcc3086478

Append rather than add build channels Append rather than add build channels (e.g. conda-forge) so that their precedence is lower than defaults.

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Keith James

commit sha 385073a2774f6ddc50afd53a2f09fb847da041e5

Add boost 1.73.0

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Keith James

commit sha 786619bc9f05c1a9e48023fbef5f79624c878e96

Reduce avrocpp dependencies Remove specific dependency boost-cpp and use our boost 1.73.0, which is built without Python support. This prevents many other packages from conda-forge being depended upon, including py-boost, python, numpy. Remove non-Linux clauses from avrocpp recipe. Move avrocpp from red-recipes to recipes as it no longer depends on conda-forge.

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David K. Jackson

commit sha 4b144175f601a12425142428acbd8bb9854f0013

Merge commit 'refs/pull/191/head' of https://github.com/wtsi-npg/npg_conda into HEAD

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David K. Jackson

commit sha 609fa0d2ce0c59c20498330ac7e791f3f74330bb

Merge commit 'refs/pull/203/head' of https://github.com/wtsi-npg/npg_conda into HEAD

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David K. Jackson

commit sha dacf47bd10fa4d66d92e3393f49857bdaf995331

Merge commit 'refs/pull/204/head' of https://github.com/wtsi-npg/npg_conda into HEAD

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David K. Jackson

commit sha 65586c5d8d3e8cb4da58eda8c65db8540bf4eb16

Merge commit 'refs/pull/198/head' of https://github.com/wtsi-npg/npg_conda into HEAD

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David K. Jackson

commit sha ac86a7fd3ad9d828607dc9ea38a3be5cf877b817

zlib download url change

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PR opened wtsi-npg/npg_conda

Zlib download url fix

Amend zlib download as previous one no longer works. Leave build number the same as checksums are unchanged.

+334 -11

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Marina Gourtovaia

commit sha 17a3fd70e90b213b9aa21733360e3ec2a7863a5c

move potentially reusable code from the generic ampliconstats class to its parent to make in available for other generic checks

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Marina Gourtovaia

commit sha 246c2cc2d801969affcf504d9afab7c0409b646e

generic check for the artic pp

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dkj

commit sha 61cd1c3894c8c2d91f16003440e75750d1d1f82b

Merge pull request #714 from mgcam/generic_check4artic reimplementation of the generic check for the artic portable pipeline

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Pull request review commentwtsi-npg/npg_qc

reimplementation of the generic check for the artic portable pipeline

 bin/reformat_fluidigm_snp26_results_irods.pl bin/qc bin/qc_db_delete_autoqc bin/mqc_outcome_reporter-bin/npg_autoqc_generic4artic bin/npg_mqc_skipper bin/npg_qc_autoqc_data.pl bin/npg_qc_tag_sniff.pl+bin/npg_autoqc_generic4artic

Should we be removing this with this PR? Or leave post npg_seq_pipeline change?

mgcam

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PullRequestReviewEvent

issue openedSamStudio8/majora

api for establishing run -> library ->biosample linkage (no metadata reveal)

At the moment we use the api/v2/process/sequencing/get/ (with run_name) to confirm that we have linked run to library to biosample and also to establish whether or not the biosample has been properly registered (with minimal metadata).

We'd like this functionality from the API without the exposure of actual metadata so that we can request long-lived refresh tokens for a non-metadata-revealing OAuth scope.

(Happy to do a two stage lookup with api/v2/artifact/biosample/query/validity or v3 equivalent if a new <something>/sequencing/get/ were to return run -> library -> biosamples[sample_id1,sample_id2,...] )

created time in 13 days

pull request commentconnor-lab/ncov2019-artic-nf

adding -f Mark reads as QCFAIL instead of excluding them to trim.

@m-bull (sorry for the late reply) - I think the code will have to change to accommodate further change required in ivar...

FredDodd6

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Marina Gourtovaia

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correct result path parsing in case of double forward slashes

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dkj

commit sha e23feafc8601c40e67cffe97ffccf8c455b5f941

Merge pull request #712 from mgcam/allow_double_forward_slash correct result path parsing in case of double forward slashes

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Marina Gourtovaia

commit sha 421a76ead99c3cd4926fec0abedfe606112f17c3

new table for ampliconstats data

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dkj

commit sha 06cd3f3ff2cb7646bdbac77b7ac44e3cf2a457c2

Merge pull request #155 from mgcam/table4ampliconstats new table for ampliconstats data

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Marina Gourtovaia

commit sha 15652eb66ab6510b51e4e3003278210d04aa3f2e

Generic: add missing standard custom DBIX relationship

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dkj

commit sha 170981b588104cc35da805b15f33db7e4c63ab1b

Merge pull request #710 from mgcam/dbic_fix4generic Generic: add missing standard custom DBIX relationship

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Marina Gourtovaia

commit sha 2dce1d2206067228d309bbcf247516e4d7a2de13

implementation for the ampliconstats portable pipeline

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Marina Gourtovaia

commit sha 24dc86d28084e6836cc873a39e3222bb924a2f27

new pipeline function - stage2App

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Marina Gourtovaia

commit sha c82c5257bc5f642d31120e0d97e646b8195230a2

tests for ampliconstats pp and minor code fixes

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Marina Gourtovaia

commit sha 84a55fbe603d01ee0f6da78d52cf6edb828bcf0e

preprocessing of the stats file before plotting

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Marina Gourtovaia

commit sha 8eef19aeaa900ef304e14a0dba7d9f2ccbb4f2bc

allow for spaces in sample supplier names

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Marina Gourtovaia

commit sha 2a2c31294b7ee69e7ff92fe775fee0bbb2e58a78

run qc scipts after prot generation

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Marina Gourtovaia

commit sha 367ee6b5a8965176cec192e219b98fb98ab0c463

values in the replacement map should not contain white spaces

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Marina Gourtovaia

commit sha 5ff03ad813f21b98bdb2a3c8ca3e3e432a39798b

configurable minimum base depth list for ampliconstats, make amliconstats qc check to save coverage data

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Marina Gourtovaia

commit sha c1b6003e5bdc277cc3da3943950079c7eecfd49b

the job should not fail if no artic input is available

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Marina Gourtovaia

commit sha 1e91170bd81084f048431857f77e181755200aff

expand POD

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Marina Gourtovaia

commit sha b641b5db150ead57091c18606eb6e931044d4653

propagate pipeline name from the product config file

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dkj

commit sha 498b0b3f3573572469ffe408182e218dd52f0c5e

Merge pull request #605 from mgcam/pp_ampliconstats pp for ampliconstats

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pp for ampliconstats

Requires a change in product config. Matching SeqQC code is in https://github.com/wtsi-npg/npg_qc/pull/709

+415 -26

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mgcam

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PR merged wtsi-npg/npg_qc

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rna_seq template simplification and db access optimisation

Tested with the viewer, works as expected.

+13 -15

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mgcam

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Marina Gourtovaia

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rna_seq template simplification and db access optimisation

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Marina Gourtovaia

commit sha 47a7d6ad09c396e38a253747f5f51bdb11e4730e

a practical solution for ampliconstats plots

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dkj

commit sha abc4486c25e0f0a398cf96a99b0efd1c2408fe80

Merge pull request #709 from mgcam/ampliconstats_images_display Ampliconstats images display

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PR merged wtsi-npg/npg_qc

Ampliconstats images display

Have not been tested

+37 -15

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mgcam

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issue commentwtsi-npg/npg_conda

iRODS 4.2.7 fails to build in Docker container, multiple errors

I recall gzip is required, maybe in tests. I built with --build-channel ostrokach conda-forge to get gzip.

kjsanger

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Keith James

commit sha f8fc74359b135f2f45abd8703095872e20f992be

Remove eigen 3.3.4 Moved to https://gitlab.com/libeigen/eigen/-/archive/3.3.4/eigen-3.3.4.tar.bz2 in December 2019. We don't use this recipe any more.

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dkj

commit sha 4e5c7f77efd5eeb6a0ac6e80737ddf9c29effe13

Merge pull request #188 from kjsanger/bugfix/remove-eigen-3.3.4 Remove eigen 3.3.4

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PR merged wtsi-npg/npg_conda

Remove eigen 3.3.4 bug

Moved to https://gitlab.com/libeigen/eigen/-/archive/3.3.4/eigen-3.3.4.tar.bz2 in December 2019. We don't use this recipe any more. Resolves #174

+0 -36

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kjsanger

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issue closedwtsi-npg/npg_conda

Eigen 3.3.4 repository at bitbucket moved to gitlab

ERROR:root:WARNING:conda_build.source:Error: HTTP 403 FORBIDDEN for url <https://bitbucket.org/eigen/eigen/get /3.3.4.tar.bz2>

https://bitbucket.org/eigen/eigen/get/3.3.4.tar.bz2

Repository unavailable

Bitbucket no longer supports Mercurial repositories.

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kjsanger

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Keith James

commit sha 19227abafc8ad3dbfa72357b8550f7e457f31d2e

Remove nanopolish This hasn't been used in recent months by our team, nor was it deployed, so removing from the "live" set of recipes.

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dkj

commit sha 369338fe472d2d9392a456d321d2d76e51a06fe7

Merge pull request #197 from kjsanger/bugfix/remove-nanopolish Remove nanopolish

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PR merged wtsi-npg/npg_conda

Remove nanopolish bug

This hasn't been used in recent months by our team, nor was it deployed, so removing from the "live" set of recipes.

+0 -49

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Keith James

commit sha 426cbe92120316ca4dff21725acd179d1eb03085

Create libpam-dev package, remove dependency on gettext Create libpam-dev. Remove dependency on Conda gettext package. This build works in our minimal Docker environment without the gettext package, so I'm removing it. This removes any dependency on conda-forge and consequently this recipe can be moved from red-recipes.

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dkj

commit sha 974ce71ac8d5efebeef7154603de83fbc56b667f

Merge pull request #199 from kjsanger/bugfix/add-libpam-dev Create libpam-dev package, remove dependency on gettext

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PR merged wtsi-npg/npg_conda

Create libpam-dev package, remove dependency on gettext bug enhancement

Create libpam-dev.

Remove dependency on Conda gettext package. This build works in our minimal Docker environment without the gettext package, so I'm removing it. This removes any dependency on conda-forge and consequently this recipe can be moved from red-recipes.

+74 -56

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kjsanger

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PR opened wtsi-npg/npg_conda

revise htslib build to not use autoreconf

as 0c3c032

+3 -2

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pull request commentwtsi-npg/npg_seq_pipeline

Another attempt to add 'showback' function

Thanks for separating out code into separate modules by functionality - I think we can push this a bit further: e.g. put thenew modules in a new namespace npg_pipeline::showback (or npg_pipeline::executor::showback ) rather than in npg_pipeline::executor space (though I acknowledge some of this is per executor - so see the + side ). We could move the process_run into a npg_pipeline/showback.pm I've not yet looked at code - only structure...

jenniferliddle

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Marina Gourtovaia

commit sha 459675de5053e13afbdbbbe68810f906e764c49d

correct child error value

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dkj

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Merge pull request #613 from mgcam/correct_child_error_code correct child error value

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David K. Jackson

commit sha a2f1691612ac22277dd1991c55aafff1b18f3be9

explicitly name variants of amplicon 1: include first primer twice seems to avoid trimming to shortest variant of amplicon when using align_trim

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Keith James

commit sha 7921224413f635c9472f20d77075f64941708146

Create bin directory on bam_stats install The builds fail because they try to install to the bin directory, without creating it first.

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dkj

commit sha 147fb08b951fe0a139ed3556072545f7a43533b6

Merge pull request #190 from kjsanger/bugfix/bam_stats-bin Create bin directory on bam_stats install

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PR merged wtsi-npg/npg_conda

Create bin directory on bam_stats install bug

The builds fail because they try to install to the bin directory, without creating it first.

Resolves #180, #181

+2 -0

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kjsanger

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issue closedwtsi-npg/npg_conda

bam_stats 1.13.0 fails to build, target bin directory not created by the build script

RROR:root:+ cp ../bin/bam_stats /opt/conda/conda-bld/bam_stats_1598376291847/_h_env_placehold_placehold_placehold_placehold_placehold_plac
ehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla
cehold_pla/bin/                                                                                                                            
ERROR:root:cp: cannot create regular file `/opt/conda/conda-bld/bam_stats_1598376291847/_h_env_placehold_placehold_placehold_placehold_plac
ehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla
cehold_placehold_pla/bin/': Not a directory

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kjsanger

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Keith James

commit sha 9222d0a0789cdee17694a37e1fe7cfb8f378b934

Create bin directory on install. The builds fail because they try to install to the bin directory, without creating it first.

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dkj

commit sha 06e4595cc888ac3d83cd52f53a9f546b0363850c

Merge pull request #189 from kjsanger/bugfix/npg_qc_utils-bin Create bin directory on npg_qc_utils install

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Keith James

commit sha 6f0ecb0ad20554916757f30408df59f24624a3f3

Fix samtools dependency name

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dkj

commit sha 06f172be5d87989fac5d556ddb891a7376c787e7

Merge pull request #193 from kjsanger/bugfix/goleft Fix samtools dependency name

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PR merged wtsi-npg/npg_conda

Fix samtools dependency name bug
+1 -1

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kjsanger

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Keith James

commit sha 96e8b3355bb4932cadcce73e78aa5352b741cbf1

Remove bambi 0.11.1 I don't think this recipe has ever built successfully - no package was added to the channels, only later versions exist.

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dkj

commit sha e01392f114060a3859b126473a02be2816c87000

Merge pull request #187 from kjsanger/bugfix/remove-bambi-0.11.1 Remove bambi 0.11.1

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PR merged wtsi-npg/npg_conda

Remove bambi 0.11.1 bug

I don't think this recipe has ever built successfully - no package was added to the channels, only later versions exist. Resolves #178

+0 -68

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kjsanger

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issue closedwtsi-npg/npg_conda

bambi 0.11.1 fails to build with multiple errors

./configure: line 3634: LT_INIT: command not found

and various confliciting type errors

ERROR:root:In file included from src/hts_addendum.h:27:0,                                                                                  
ERROR:root:                 from src/bambi.h:25,                                                                                           
ERROR:root:                 from src/i2b.c:19:                                                                                             
ERROR:root:src/cram/sam_header.h:242:10: error: conflicting types for 'sam_hdr_dup'                                                        
ERROR:root: SAM_hdr *sam_hdr_dup(SAM_hdr *hdr);                                                                                            
ERROR:root:          ^~~~~~~~~~~                         

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kjsanger

pull request commentwtsi-npg/npg_conda

Remove eigen 3.3.4

nanopolish depends on this? Remove that as well?

kjsanger

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David K. Jackson

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David K. Jackson

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David K Jackson

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David K Jackson

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Avoid shell (layer and expansions) when launching commands

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David K Jackson

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David K Jackson

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David K Jackson

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David K Jackson

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David K. Jackson

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David K Jackson

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David K Jackson

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create barnchdkj/npg_seq_pipeline

branch : climbup

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David K. Jackson

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pull request commentconnor-lab/ncov2019-artic-nf

adding -f Mark reads as QCFAIL instead of excluding them to trim.

We're on hold with this as it still removes records that we would like to retain (but mark as QCFAIL) for reanalysis.

FredDodd6

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pull request commentartic-network/primer-schemes

Subset of nCoV-2019 primers to create 1k amplicons

nCoV-2019-wsi1k_1_RIGHT_alt actually goes into pool2 and nCoV-2019-wsi1k_1_LEFT goes into both pools - but I wasn't sure how to represent that for current pipelines to use effectively.

dkj

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Primer schemes for real-time genome epidemiology

https://artic.network/

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Keith James

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Keith James

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Fix test failures on CI that do not happen locally Add iRODS 4.2.8 to the test matrix. Check for both libirods_common and libirods_client for iRODS 4.2.x. Use the available replication resource in the test server Docker image, rather than manually irepl to another local resource. Use check library from Conda, rather than building from source. Add reporting on failure.

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dkj

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Merge pull request #227 from kjsanger/bugfix/update-travis-build Update Travis build for iRODS 4.2.7 and prepare for 4.2.8

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PR merged wtsi-npg/baton

Reviewers
Update Travis build for iRODS 4.2.7 and prepare for 4.2.8 bug

Add iRODS 4.2.8 to the test matrix.

Check for both libirods_common and libirods_client for iRODS 4.2.x.

Use the available replication resource in the test server Docker image, rather than manually irepl to another local resource.

Use check library from Conda, rather than building from source.

+48 -42

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kjsanger

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Marina Gourtovaia

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specialised generic autoqc check for ampliconstats

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dkj

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Merge pull request #703 from mgcam/generic4ampliconstats generic check for ampliconstats

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generic check for ampliconstats
+62436 -0

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mgcam

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Keith James

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Bugfix: stop IPC::Run process pump before exiting

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dkj

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Merge pull request #206 from kjsanger/bugfix/groupadmin-shutdown Bugfix: stop IPC::Run process pump before exiting

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created tagwtsi-npg/p4

taguntagged-2312a0a435db4d5f73a1

Process and Pipe Pipeline Panacea

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Process and Pipe Pipeline Panacea

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David K Jackson

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add group namespace in ACL for pp iRODS archival

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pull request commentmgcam/npg_seq_pipeline

add ACL for pp iRODS archival

group may need a #seq suffix

dkj

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pull request commentmgcam/npg_seq_pipeline

add ACL for pp iRODS archival

Did not work in seq-dev testing.

dkj

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PR opened wtsi-npg/npg_seq_pipeline

portable pipeline iRODS archival

Built on #606

+1339 -3

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mgcam

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Merge pull request #14 from dkj/irods_pp_on606 iRODS PP - sample supplier name changes

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David K Jackson

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add ACL for pp iRODS archival

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PR closed wtsi-npg/npg_seq_pipeline

Archive PP products to iRODS

Build on #606 but:

  • cope with no sample supplier name
  • use sample_supplier_name instead of supplier_sample_name to match existing iRODS metadata (evnen though columns in warehouse iseq_*_product_metrics tables don't match)
+1406 -29

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dkj

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pull request commentwtsi-npg/npg_seq_pipeline

Archive PP products to iRODS

changes adopted by #606

dkj

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PR closed mgcam/npg_seq_pipeline

sample supplier name: naming and absence
  • cope with no sample supplier name
  • use sample_supplier_name instead of supplier_sample_name to match existing iRODS metadata (evnen though columns in warehouse iseq_*_product_metrics tables don't match)
+96 -31

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dkj

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pull request commentmgcam/npg_seq_pipeline

sample supplier name: naming and absence

replaced by #14

dkj

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