From 379c4b870725dc9338eb390d08fb876ae9f87f38 Mon Sep 17 00:00:00 2001 From: Pauline Ribeyre <4224001+paulineribeyre@users.noreply.github.com> Date: Fri, 23 Oct 2026 17:08:13 -0500 Subject: [PATCH 1/3] DPoP proxy doesn't need GEN3_TOKEN env var --- docs/howto/dpop-proxy.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/howto/dpop-proxy.md b/docs/howto/dpop-proxy.md index 7a9e91b4..c3ce5d02 100644 --- a/docs/howto/dpop-proxy.md +++ b/docs/howto/dpop-proxy.md @@ -130,11 +130,11 @@ process { } tes { endpoint = 'https:///ga4gh/tes' - oauthToken = env('GEN3_TOKEN') + oauthToken = '' timeout = 60 } aws { - accessKey = env('GEN3_TOKEN') + accessKey = '' secretKey = 'N/A' # pragma: allowlist secret region = 'us-east-1' client { @@ -298,4 +298,4 @@ above it explaining the fix. To see more, run with `-vv`: each proxied request logs its resolved upstream URL, the response status, any nonce retries, and the full response body of a failed token -exchange. \ No newline at end of file +exchange. From 48666f1f5258fde543b2172a3cd35060121f09bb Mon Sep 17 00:00:00 2001 From: paulineribeyre Date: Fri, 23 Oct 2026 22:09:01 +0000 Subject: [PATCH 2/3] Apply automatic documentation changes --- docs/_build/doctrees/auth.doctree | Bin 32367 -> 32393 bytes docs/_build/doctrees/file.doctree | Bin 39346 -> 39372 bytes docs/_build/doctrees/index.doctree | Bin 5410 -> 5441 bytes docs/_build/doctrees/indexing.doctree | Bin 153130 -> 153156 bytes docs/_build/doctrees/jobs.doctree | Bin 26219 -> 26245 bytes docs/_build/doctrees/metadata.doctree | Bin 139418 -> 139444 bytes docs/_build/doctrees/object.doctree | Bin 12596 -> 12622 bytes docs/_build/doctrees/query.doctree | Bin 39709 -> 39735 bytes docs/_build/doctrees/submission.doctree | Bin 102792 -> 102818 bytes docs/_build/doctrees/tools.doctree | Bin 5182 -> 5205 bytes docs/_build/doctrees/tools/drs_pull.doctree | Bin 137062 -> 137088 bytes docs/_build/doctrees/tools/indexing.doctree | Bin 99831 -> 99885 bytes docs/_build/doctrees/tools/metadata.doctree | Bin 36466 -> 36500 bytes docs/_build/doctrees/wss.doctree | Bin 31814 -> 31840 bytes 14 files changed, 0 insertions(+), 0 deletions(-) diff --git a/docs/_build/doctrees/auth.doctree b/docs/_build/doctrees/auth.doctree index b550b07813004684035d41b69e6ee3ab53cd2d6c..d0f636f1aab4098e61f7dabf018e057084b1dae5 100644 GIT binary patch delta 59 zcmV-B0L1_A`~ivm0R(^rm42}VoO%rkY-ML*V|ia`WOI~=v!8ko0t;v)eUxf23IG6T R3zOM=MU$_5E3+MaQUS(p7IXjr delta 33 pcmeDD%lQ5eBTED8)Rc`ZbE-D4tKwst%w4N9`9zJ&W{cWDMgaPJ4afih diff --git a/docs/_build/doctrees/file.doctree b/docs/_build/doctrees/file.doctree index bd794497f00197c65be7e57964fa516ee7ec9424..a61a720c2cfbae4e9329ea93dbbdd7d9fe6ce78a 100644 GIT binary patch delta 59 zcmV-B0L1^YvjWVs0tA2smBFzD)s+njY-ML*V|ia`WOI~=v)Gjn0t;v)eUxgw4FCXW R3zHIrVxS2UBafDF9-)Q0sz567?%J5 delta 44 zcmX@8wMdJlfpx0*MwSY}&0T_gOp|vBn+jwo)K1aJXvpBsGG%07$Y|aCPB@qm06#Ph A-v9sr diff --git a/docs/_build/doctrees/indexing.doctree b/docs/_build/doctrees/indexing.doctree index 3fb622e2755227ac4b9f12ba32096067a3e5a98e..a235ef7de1942f5bbfbc48ec9d4a713aa94b2b90 100644 GIT binary patch delta 68 zcmZ3rhV#f8&W0AoDNKrt(p#07JOg>Ta#GV1lPlvhQ;Mf_Y|jd0;%DN{P^q1gm0`ue YkioruNidTs#&W0AoDNKrtj9ZnMJOj5^1~Tz6O+OaGq_cf;Fp~-6_Rk?qfs6n%b`7Ec diff --git a/docs/_build/doctrees/jobs.doctree b/docs/_build/doctrees/jobs.doctree index 7e2ece1845afe5a31ce2488365cb622f79d816a0..dcc8a87dcb1a58efdb7bf5670d6e3e3347b7b7f4 100644 GIT binary patch delta 59 zcmaEThOzZ5BTED8)T)gvElIpwIjQN1$(8Y$DaBJdHn%77GjV6A)K1A_;bdUQ;GTRi PC35og6z$EDsX>eYnphPR delta 33 pcmZoY%lP^XBTED8)P#*JElHcFCGjy$W>3|bydfoGvq@?oBLL)d45$DA diff --git a/docs/_build/doctrees/metadata.doctree b/docs/_build/doctrees/metadata.doctree index 53c986e5a7a09fcadede0c573377d70794af123f..e96151249f7c71a967fb44c62fa71f0ab8ba50a8 100644 GIT binary patch delta 96 zcmV-m0H6Pw!3ea$2!MnElmZ zaWnt`XbZQ690C^sms=bHE4P~+0vQ4V3^kKMWi136Y6&%yVKN(+0w4lE0SA{tAOcv1 C{u(3z delta 64 zcmdmTkYm14-L UU1q5)_Gt=C(TuFqV-%Po0A2zRl>h($ diff --git a/docs/_build/doctrees/object.doctree b/docs/_build/doctrees/object.doctree index c791cd2702ef1425193860c3a84b67bf6543d3a8..baa38775a9621e95a8e2bfd0b26b775e3cf8cdf1 100644 GIT binary patch delta 81 zcmdmzbS{adfpx0$MwU)pUap+f^u*-K_{@~zDIJ@8borUoGgNA)WW8f%V94Mu&QPeG iqLK9)%*n9KaLW3_$iR@r$i%=%_{yo@}(yj(e{>50je@tG;bQ#!Uw^fK}@ac8L1PRZ&~W?;zR Vo*vZC_;k8PKcn_`vk8nri~z^<6&nBm delta 39 vcmZ3qn5|$Wbyo@}(+tqs+`Ix4wOkmWR?%2=xWP9KQ#y~~@0gMcq diff --git a/docs/_build/doctrees/tools.doctree b/docs/_build/doctrees/tools.doctree index 81b49913866249ee75485afae740058c1cbb1bc0..5e050a6fe022575fcaa7ad0a650c36744ee66d49 100644 GIT binary patch delta 100 zcmV-q0Gt25DAgzgfCZIGu>`FT4GL^!XJKP`Uuk4>l!&vi4-WztXe51`FTv%e1x0+ZwsBMxXFeUvC@r)Udkm}s1Jvj-BE0Rcsm Zo)aSkLID5(lRpa?lim|N0YH-*6gmus6!riB diff --git a/docs/_build/doctrees/tools/drs_pull.doctree b/docs/_build/doctrees/tools/drs_pull.doctree index c0dea75be14170e262df98868dbdb0f931189623..c889324aa436fd23e893570084d7489a4b8bd9a8 100644 GIT binary patch delta 87 zcmaF1j-z2cM?(wa6ec4MH*p3qnC=+EXtFhrX{jJDS59hrVsd4CW=iptj_pE1O#DpT o87j3?vS#TsFl2B~_Yq<8XB6B%M}(=8ak`QSllFEIF{U6!06tn5IsgCw delta 61 zcmZoz&+%*>M?(wa6ec4M9dQOQnC=+EXtFhrX{q3LMIk0Wrs+&#Oghu8MVR~;g|~N! OFjX>c*B4_7WCQ@|hz@iB diff --git a/docs/_build/doctrees/tools/indexing.doctree b/docs/_build/doctrees/tools/indexing.doctree index 226661ff725b92f5617fb04eb0e554fba1587b03..00edc01af0ca1f3508ba6d96e1afbbff3cc4c721 100644 GIT binary patch delta 1099 zcmaizQAkr!7{~AbBqI_t(PneIGpEsL6^=*(--4b*?KzTBCc7Tj?wxa?L~Yrw7zq-N zzDQD#!d@hZWD!EW^%(SGf)En)tPx2R(%H^EYiiQdx##fx{{R2|&UZHNyA~!~nOBGd z`Me3diB=tm^+m7rjzs#eC3EBXU_Ywaaiir{F35lSG|i~wzg=QE!5oB z1e#ScGf_-7nLrDj8$eI~Wdb#T{V;_HK-LgWu`Qj#X?TU0nM9j6E20<;e3XgBYwR<8 z#wA1VXi8n>HoZ&Y1$;#e9%@a)C#cRe>QB!KYN8_6AMeX`G*7saW@@mvFURdenwBzx z+!4K7E4D(YXx}Dv&L|z>?q=Lgp%HlMj{Sq8^%UlDQDU76E7*$;{JH^u^$r`EmrEeJ z185)q3slsV<;u$XJF31cSII#EGSZABrWLWPBdvROL=RFDxETCkLzr)Bl*Fb z=!Tk!^$gaqDybDkb=z=L(`^J)I~JY4lkM1)<=<8LuCVQUhAjydE`rrG7AKt@Y*h2( zT*Z?N{0+`keDJF=>N51M!rjY9P)N=~jzX}cAhOr94L{9fp#M)|d=$&M4gu(IAC@A`}#>feHct06lmqhzLOxJe3L}f?zkhGqWc3$90*{d*3&2c4_?48OmHmH8w;9uet?Q5`XqX4Vu`&Hs7ZG%7d^2y zp=~yXWu!B<8!2JqK;w&zUdU=IlNe*aylU(xuddHWm{Frv7JKPs2K$@@?=uL?W0;YyVC9KN#AYl-xRhaTwXaptQxY@xjF9(x1gNJxiJ0D zelLW3rkvj|96at`PUF!HjH}fR713hv1Y1??^i7<)0GWKIgnX`RLBw!be>2(D`mun~`W>N7PALZ^I^in8El4RDoGJ diff --git a/docs/_build/doctrees/tools/metadata.doctree b/docs/_build/doctrees/tools/metadata.doctree index 2e360db384eb2c2210f281d985d78e1c09a4a860..19f7300d8dc2a7714f53dc33a81e6bcd65ca85ae 100644 GIT binary patch delta 313 zcmew~hiS@OCYA=)sht~HBAa-*a#GV1lPlvhQ;Mf_Y>sK-XA;g(shy&c^@EFnA%i>X zBZ$(PyrQLoF@LgRtM=ra7Te9t^d?RJbaC;PTb zGR@+i{4rd5a&vn((=LRv?Oo4DQJv!=)!LZSQ8>0amdUtb!?P-Q=1M3+d_H3=A1kS>a4T zN;-o%Lnb3CL)Nb}DGRFaRfjXrV0}_q>wr39r}VJqq?V=TOz~#!VJWFBNS%_k zY4XHQX|ScDYzn9byagNZil71KdnDOJOEWaGrf*)^mBa{hJJ1bGf;^Kqx~Na~k78xw V;{kaQpF_^~$T3de{H|viBLEs`bw>aI diff --git a/docs/_build/doctrees/wss.doctree b/docs/_build/doctrees/wss.doctree index 95fd0aac8bfb69b9f0ec594f736d0b4f53adb133..29e15ff132db077ac82c3fec597d516faaae2c2d 100644 GIT binary patch delta 59 zcmX^1gYm%+MwSNFsi7NLyeoLQa#GV1lPlvhQ;Mf_Z1$_*XX4IKshyJL&&|M)!9BU7 PDtB^RmG Date: Fri, 23 Oct 2026 17:20:45 -0500 Subject: [PATCH 3/3] we also don't need these --- docs/howto/dpop-proxy.md | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/docs/howto/dpop-proxy.md b/docs/howto/dpop-proxy.md index c3ce5d02..05d41427 100644 --- a/docs/howto/dpop-proxy.md +++ b/docs/howto/dpop-proxy.md @@ -129,17 +129,11 @@ process { container = 'quay.io/nextflow/bash' } tes { - endpoint = 'https:///ga4gh/tes' - oauthToken = '' timeout = 60 } aws { - accessKey = '' - secretKey = 'N/A' # pragma: allowlist secret region = 'us-east-1' client { - endpoint = 'https:///workflows/s3' - s3PathStyleAccess = true maxErrorRetry = 1 } } @@ -147,7 +141,7 @@ aws { workDir = 's3:///' ``` -Run that with `gen3 nextflow run main.nf` and the generated override changes five keys: +Run that with `gen3 nextflow run main.nf` and the generated override sets five keys: `tes.endpoint` and `aws.client.endpoint` become the local proxy, `tes.oauthToken` and `aws.accessKey` become the task token, and `aws.client.s3PathStyleAccess` is forced on. `workDir`, `region`, `timeout`, `maxErrorRetry`, `plugins` and `process` are yours and are