From 6e81f73c09d66f86e1babe911a1989991c1d1c56 Mon Sep 17 00:00:00 2001
From: Thomas Cokelaer <cokelaer@gmail.com>
Date: Tue, 7 Mar 2023 21:34:53 +0100
Subject: [PATCH] Update metadata and singularity

---
 README.rst                                    |  17 ++++++++---
 sequana_pipelines/bioconvert/bioconvert.rules |   2 +-
 sequana_pipelines/bioconvert/config.yaml      |   4 +++
 sequana_pipelines/bioconvert/dag.png          | Bin 0 -> 4742 bytes
 sequana_pipelines/bioconvert/dag.svg          |  28 ++++++++++++++++++
 5 files changed, 46 insertions(+), 5 deletions(-)
 create mode 100644 sequana_pipelines/bioconvert/dag.png
 create mode 100644 sequana_pipelines/bioconvert/dag.svg

diff --git a/README.rst b/README.rst
index 08c6e75..431c4d3 100644
--- a/README.rst
+++ b/README.rst
@@ -1,7 +1,10 @@
+|Logo|
+
+
 This is is the **bioconvert** pipeline from the `Sequana <https://sequana.readthedocs.org>`_ project
 
 
-.. image:: https://badge.fury.io/py/sequana-bioconver.svg
+.. image:: https://badge.fury.io/py/sequana-bioconvert.svg
      :target: https://pypi.python.org/pypi/sequana_bioconvert
 
 .. image:: http://joss.theoj.org/papers/10.21105/joss.00352/status.svg
@@ -11,11 +14,12 @@ This is is the **bioconvert** pipeline from the `Sequana <https://sequana.readth
 .. image:: https://github.com/sequana/bioconvert/actions/workflows/main.yml/badge.svg
    :target: https://github.com/sequana/bioconvert/actions/workflows    
 
+|Codacy-Grade|
 
 
-:Overview: convert NGS format from one to another using bioconvert
-:Input: whatever input format accepted by bioconvert
-:Output: whatever output format accepted by bioconvert
+:Overview: convert NGS format from one to another using Bioconvert
+:Input: whatever input format accepted by Bioconvert
+:Output: whatever output format accepted by Bioconvert
 :Status: production
 :Citation: Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI doi:10.21105/joss.00352
 
@@ -116,3 +120,8 @@ To contribute to this project, please take a look at the
 `Contributing Guidelines <https://github.com/sequana/sequana/blob/main/CONTRIBUTING.rst>`_ first. Please note that this project is released with a 
 `Code of Conduct <https://github.com/sequana/sequana/blob/main/CONDUCT.md>`_. By contributing to this project, you agree to abide by its terms.
 
+
+.. |Codacy-Grade| image:: https://app.codacy.com/project/badge/Grade/9b8355ff642f4de9acd4b270f8d14d10
+   :target: https://www.codacy.com/gh/sequana/bioconvert/dashboard
+
+.. |Logo| image:: https://github.com/sequana/sequana/blob/dev/doc/_static/logo_256x256.png
diff --git a/sequana_pipelines/bioconvert/bioconvert.rules b/sequana_pipelines/bioconvert/bioconvert.rules
index 66adb08..6d98ac9 100644
--- a/sequana_pipelines/bioconvert/bioconvert.rules
+++ b/sequana_pipelines/bioconvert/bioconvert.rules
@@ -60,7 +60,7 @@ rule bioconvert:
         command= config['bioconvert']['command'],
         method= f" --method {method}" if method else ""
     container:
-        "https://zenodo.org/record/7034822/files/bioconvert_0.6.1.img"
+        config['apptainers']['bioconvert']
     shell:
         """
            bioconvert {params.command} {input} {output} --verbosity ERROR --force {params.method}
diff --git a/sequana_pipelines/bioconvert/config.yaml b/sequana_pipelines/bioconvert/config.yaml
index be55b92..bf2e037 100644
--- a/sequana_pipelines/bioconvert/config.yaml
+++ b/sequana_pipelines/bioconvert/config.yaml
@@ -11,6 +11,10 @@
 input_directory: /home/cokelaer/Work/github/sequana_bioconvert
 input_pattern: '*fastq.gz'
 
+# ======================================= [apptainers] ======================
+#
+apptainers:
+  bioconvert: "https://zenodo.org/record/7704649/files/bioconvert_1.0.0.img"
 
 ##############################################################################
 # Your section
diff --git a/sequana_pipelines/bioconvert/dag.png b/sequana_pipelines/bioconvert/dag.png
new file mode 100644
index 0000000000000000000000000000000000000000..c188f7fb296fa231e90c380c8886649a32820586
GIT binary patch
literal 4742
zcmb_ghc{eZ`yD~_-g$MR6E(W%VHie_9yOv(w5TBoqBDXKB^bRM-DnA7L~qgisL^{1
ze)Im;_x%Uoy6fC?*E#Fl_1x##XYYM(v_43agpiRC0059^y-+j2^p2R8iT@aL4_Y@a
z!gP=AfSPK6hkvi!_Tn!90HvIknzE69)_!&X#K^b<rPS0^&|2qXQVVzqiOj9#CLB}7
z)t2HB>n-Met@2zG<;A7A@p7YXJw6|8mKG*E)%^X%lgG>U3zho(C(qCFlu57)BEuDu
zNNS-zX~W}-mv>|9D#c%tmiqSB-<KKqdXLC-p0;kyUoLqME5x$Jz@t7^=*QP%6ISuU
z`^eR)8Q{lL-&>aIQW{|f9(-Fmmke`m?mn|Z9Y;cJqlD(f{MgaT(FKon?IPbkF(fu5
zCzo&J^S^<M><XgmHuZQ91vS-51uV7Wq$1UeehNwmsc<$ww7#=QxmgN~VO&CQUF2j9
zm*Yylo%4q`fN{#tJme@#%zj#%S2~pim05iwe~Xm%vNI8zke(3A^oXu)^`*l-x7el$
zVveRrcgpHrs0q*!2Wcur_G~9I%b|o&R~_ym%Nd>Cl-rS`Oaamd@3wIkYureH)D+Of
zOvSbQBC<knK4rd&xFIy`<`;`)*LKn3)G$hywKm@o&u<UFh0A@)8m&iB8r|l0GZ4eU
zaT2)by5}l@^-p4HR(h)7Q=y|jj#9MJv%bmGf2<4hnpnbkb*UdDS7qQ0W2!~16}%Qq
zF*ENw=mGh2eduF7Nc<`zYm35-OH%_P&kvg>%?m*3iw^KuV-+nS{#3+Jn~nJ<7}tv^
z*>EKte-K5FuF7Pdyu!Uw%hXevu#9hSmP&48&&-&jl+{ZQD~ogA6Rr3=R7QtpsV(}m
zw#rLkYH+WxO7H|n7qIdir8N8YzFZki#;*<T4l)oD;Bn%fW~@3#l-m=vYmZP7xDuG)
zVjsPl_?+&(iG?QR)qd&xb&^zz<Xg|9iAPE;vW@h`%qV8)EWl?@?n)Egh=nHM?Jw5N
z0VMdn0O=$c44kkxssGLJw~_}04K72L0++ZGVtJi|hP5Rlc6xVori!m;hY%4OqmZB;
z1ArSm{%~*^+4GjdF;ug366On>v3v-W)@Wfr)A$(92GE`dT6I~e@pVFACAg9kaT9lY
zOEX+AXnLr-e*?0%WrdAPZXgte$X3EIY4^YB2LmV1N`I7w<&RVp75DNDs;AIe5Up&#
zH#uS*%ZRlSs+=+@eo6-p+*1fc(;6PJhV0XX2?xOp(_?u<L;~KG{SbE=%q=PDGkoaf
z8s6Alxbs)<7;|=Vstq{Z6oCFNS&4}<Ffi!)M5gG^UCT&O)p{UHNJtp$q{lGCp&I<8
zf3^E_%T7@yJ`oY8f<ktC(53dPJ64<X^YaQb#K)N#v)*_nRDY^~i-$*A*N~I=_4Rc@
zK>;}h#gA?>B^^yoRL%Hsy67k8oRGBZ(=94m+TQhFUuF^ZcmU6~<HzF8vY{eMzJI9S
zG-UMmYXj!y=YNfi@bK{weEFqjVnSQ2m*ZFaFepCq^xc7_imECF&WG`F1CvVg2sV5N
zC#OKGG)1b7%BH2Y>#dw(Br+rDpyl(tM{9g!WF!_^*rG9RYRZK4AL;KSN)I~5#xycA
zG6w!25b5pZq4Vv<ewM6nOk5nX-{F!%MLi%QBBJeV9GImLl(w*7>E-1`t`5CDXiYph
z@xr`<?WYhgukFD?3l|R$c2Z{M0Ky)1wVCND?Y&9t;^N}q>}=m;^Y{Mvp!M)%EmmZF
zeEcJCjDv$ijpG2V8W@w3p4%?!Tg2Z!g|!pT%c$z#9dk;r^^5d!gca}3CO}(7I$t?D
z?k?uxyfJHgvvogpGo_+2&pe<ka;)RYQbU7<+FCIRa#vT^pA*G;v0?suGor9yVOZk`
z?0k0`xH>d6#KC4_Y8s1KG>|4lHC^$NGX~B(x9=y)$EPL8&rhiirY<ilQ+r-fS_&PX
zcasto6x5OT*-mnJh@i8EoCt7osxH(z4%7?)snroZe?J*bac{C_bp`ts7ZepC|Jqnt
z?Ne5ll@Z2kaNdbwRU!ZI^HtQ=QZ|?m6=;1~0L^Q<xmEa7Ov?pw3(}&tla0$w5Wc%6
zfq{WD4X$)TLP84xTiIb~@Z+TP^e8rb{EuPgmA!6Kz{F=^(NsLvjq+_joZ)9y`m8*9
z-yHt>Pm82dJ<<98ron4-kYQ)x7>z2dSzmW>lVZZ81R}Q&F>8jf|M>BPnvTv;U;lgi
z<&ppaEF~peyAX~*P=Kkk?>##2{C-8UNjI$;@h?xof^R^xb<Sk&?(S_T{Q^d&reCtN
z_bEjrB~vp!JHBeNhNK{ovSnpuW_3;^z%)U2Ma6HJxRO&-fByMh&L<*L+|ZDUDGJ!q
zGI+MW8)=&wgF%UP=$)_P{gu5*wY5-$Zk9B(5C}_#!BAuQnmc=Y>%}?mIppLr4-O8L
z-Fs0e@9k0c3X}3%+-FINiik(@XQQg}r-R~LTwFDnOf`BggLDSJ-#O1Wx^r@Ig}Y1?
zL7`A(J39^xG7bE}U<$)xkmDF!9a9bibMyYTfYZoSKj{kdh8TsQi=^b_u8Nm+SzUxg
zL|Q<g{jX&1p5ES*8T&*i45q0+y0Qq;Q#hx#2|mURY+vGO5P`942qY{KJ$KqBsfZrA
zl*NwtFgtD1<?37gD2eq!x=vLjrc{E(F^VIG7_0_m7lvcVYUQe=dPPZ?nY|RLzd8PJ
z$9Wm@=%D`H)odj~x3$tr_TXW5Q9Y%ED2LBA=*`{U)J)Mq^2z?g4rXvY*8wnWF=80{
z3cvH?q0G21HDrMsF=zHKcNH-fYonAJAGV#Rd!LZBlNkBQAPcJ`b$qYS4mkRW(K;@<
zGgVXBs-&}~M{(JeHb8rJr_aNF1n($*=88e=XQ}}x@~H>+*&Sy(6m5Ka{J2CE#8-Oy
z^PpF>xUJmAGW;MplKw8=g~`29N(m{`I5T&}vIx)jKCRkr9V0Y{Nn^)QmPR|c^mqcc
zYkZG9?wlN}+Q|OZ)Z4iWtc2*&)2=Ntde2eXyK2rl`r>$OTbua~<t+nV;zYC+%KvuH
z0#Kq4rOW*MCTWe;h&nsh-hIv7rEA@JDCfj+0QMg8?#vr`E3xZp4SnpjOy~WOWT+Fl
zcdI=a@2uN}Hkby!3c<=8aW_EPF09z1l<&>X@yy*5j=Q|Ow-8)wjqDS|u5UlJZ$6;2
zy*+{2Htx-lzY%0fxxk|j^Z8$dgXnT3LI*E4?Mh!Bm)FSr^;qB>PYiw<*-qR?0mNl`
zGYym!ZOC<kx`+ZfLsipd2M2)k3Nva<%T4<mp^Og}8L~WV5Yx%U1&UOK3eh=_$|0|+
z%YQtxL%wjP5$<G}jEYU9g92a3V*G=et9|ceTbeZjW?~^=yy(okE3Kv#L?ARp%ePP<
z3Z-j}dC6WC-}B?>wM*$8b0PJlXC9(yY_Y)pF(v@zt49Y39jJZQQq*pU?|kd^@L!=;
zi+69!ZYMXWuAnbmsRJ|7U9KN3Q5jZRI*e4_DqE0pmpq^*8gguw0(7aB0>3KFExRRl
z%48Uzv1Sly5oR#7zyaXBzaA0DXabGe=`(0eawjv&N2jb%R~I+ms--|Tk5;?Kn>Q>x
zS{%dMk6AXD+W#NTF}z}G6zY-xHG5GUs?=bI|3dwLHMw?AdLfpZm-nHnDwgTTnGg=i
zaI8kT5&zoSntu7`Z&!TJ9(laiUY5P=<`xwNn{UYJ<2R#V8tA2=eUD%natNG0UV}LD
zM-$26h%J%Hz}GM;+^lEx^f5_E<Z&ALIqk;^`Q|CBy<eEH_+qT9c_bvxYL6cskKtnR
z6I$L2<CBr`NK5<oNqceUs_%3rYCRl1=eAWJ+wn=)DZ=W;QD&2s4g6m7oXuAK!;izr
zs3?3N*+rU*-gh|lyklcy*dFcFeTl;O5U>Oz35JJ2TSojeU@(|-9qNhy8vOmdDk>(1
zu&*i=*uue_d@&4?CH*HCy`qfN%jumP4Xdo93QlS$`RyhAjPAHguIKEx>9*dtvpL}~
z?P^VCMs0lq%A0x#6)~~V-k;Y!7y4Jm)UJk9x~w7L0f*K-?0%uAX;asyJ6ZA!#-?<L
zhzNWsB_Vl!eEK3Cb}>1o?#WVE;-QPwJ-PbcPF_oM`sRqDH-#z{#Rp+U7T?#r#ACw{
zyjBfWppV4ky00t4pqv?;8VkWQDakPl)6X+{+ey3CJWqJ=Dp~ny6zK|!kr^4L)_IqE
zFL$zpg%ge}Jh>gF1UoImI}sLwKL5x^1zdW_k}@Z=w0<-J?v)vbkFff4d*~gP@@6|a
zPIlbzUl7UJmB(vv93o?*)MLM+S|byvt$6edZ1kT`kL8ccOsxIvsj}RulUsI%*Y7V5
z%y!-zBZpL-N1j|Xb*eK{t`VJ{s8G9H-?%c~-(SW~XMWWRe&3-NejLr47DHI}aK_VP
zjj|i>xZmib0jlFRFiF{pXJSS5^>b|A-?lgIo{JYYb$pvU-{n@eJ3WaS8elsA2-uz&
zPp|RFK9i8PvDDeEva+5(2T_C9_cA^0T)iv)xSO}pW8$)wqj|C2o5-{Ji-$s3!fdz6
zEpIDXJAucaTYLU;*`7}X?>l5jvS)KMa6=~-o+B2KPBbliaWUTPTW)$GPy2IeQMWr{
z5Vs*?29JeaQc_UwsgT+8qXI2J{lgg*COs_kC(YDDK^L~}9)8mG4g|<>(GJycHtBX?
zrqbP{y&+5NI5McIo31jguMnu<XDdPRH`c~BONu0HxchT9<LJQ(ly|D=2~t1+3tvl5
zlex(4_n79)LQ4WRxS+j$l9P!g+OD)D3CS3@v%}&jZ!S8V{sHo8ueK1rCWgT4<pd)~
zvY-jK)*ghUMu7@*SN`8yvKDGrwK!Z|%Y7;cR<H=~Rf1LroNa*1R`Qe^;|Ko6`bnA$
ziB3j=C~M&hV3BKc>XIv&!(?{y*RQ`ehcfZ*9%9B!pRo7|BrHySi~Cm_F@(XDtM;qE
zUxge8vrG8+_}Y%Th;U~1zQ3Z-$1aG8jm4^&b^AxwC(3ak4VsbBA44OcF(bZAssB!!
z72|xriaY-+)W;YTn^-TW$djvfz4D3dg`OS{7Z;8)dEdxLF*4BM()SDxi?hGQd&{gN
zSY~&sGQX;dv~_V9W55ySm7Mz-BLwtdL0Tfe*6gDrh>t8YH#fK2Li5{##S<c|Q@9=o
zw7CJZak@U)$WjXZc6R1-&~^%Xf3^A<>Nm876UPg1ovw1+pKJIOiSbdy*P*%OPZO&V
z;s4S9Z_!@A^x^l0IMl*v(JQOTCM?l#q{9!!R<f;6akMv1%x58cUUZ3SW7cA0b;U)!
z`Ei=!A&&542m@uJ8iBSJG(ku+!9V5rH3q3Hu0SGyvX&Oh?9mJA5Oc<lCPdPaulX$t
z?oh0S=#CEo2Wzu(+`RbcI0k?Zvl0lF=!AYO?<ZF&_wLcK<GL`5X|yg8oi-|7UHw}I
zgK_=d0-x?D{A_VlsmeMjORQbGEDic>C(M4q%_7Xt<%-Zk6Hk{l7!Z~_LGd+vA0brD
zm?(-l30Sq|<vwSOP}(F{|FayRnITUTfMR~#PG7K{%8NWkiwc?Jgf$dKWWa1L`~l`{
z6V2{S?zb0Mx$&`_VgdsKLDui;)T+%sto|v-+ODc7@Id#9a_bDhY_z?>Mvt+hU8gzx
zTPjkg;rNUs$9nP~4!UwT6F%XUnm3WU+UGYFZNx8v(6@(%Hu@`9HiaDbmz|o=-nUH`
zg-9iKTrSAGx&P~2dXXpkHR{&@r-b+f-KL|up1aU_=q*$B!wua^y0qlM>SuyXaTL!*
z2y!jFvOOC~!n7?PY$og6eDel=*qO63X=LLlZZ|XNl%aGRmnPDgBFp?cFON(9nhQg|
zIUDHHhL>vPslAuW#T(_-S%FEPcyu{1%y;&MCm;9%GN=H%?lErtsp4tRxyYk8jtEuS
zzr6(R;)dlra~?o7M-!N~CW7x8>y0pRkwirJG$UR<&&`dFVhg<X>heJT5~(Bo+ktQ4
z{E|UP&TsVXO4vlTAUOd@m)mVgzRROyw))hoYQ}{5;=n_YhQ`O#WPE;f<%$$@j*6~O
z&?ubFCne&1y{2|%Sd_cdWL?;a-+X7-`{?BTL<0C<wSIhMTac{}*?hpNvkXbqAbMSk
Q`LP7hQU|G3sn~w}KXn8-F8}}l

literal 0
HcmV?d00001

diff --git a/sequana_pipelines/bioconvert/dag.svg b/sequana_pipelines/bioconvert/dag.svg
new file mode 100644
index 0000000..fb7f544
--- /dev/null
+++ b/sequana_pipelines/bioconvert/dag.svg
@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
+ "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
+<!-- Generated by graphviz version 2.38.0 (20140413.2041)
+ -->
+<!-- Title: snakemake_dag Pages: 1 -->
+<svg width="76pt" height="116pt"
+ viewBox="0.00 0.00 76.00 116.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 112)">
+<title>snakemake_dag</title>
+<polygon fill="white" stroke="none" points="-4,4 -4,-112 72,-112 72,4 -4,4"/>
+<!-- 0 -->
+<g id="node1" class="node"><title>0</title>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M49,-36C49,-36 19,-36 19,-36 13,-36 7,-30 7,-24 7,-24 7,-12 7,-12 7,-6 13,-0 19,-0 19,-0 49,-0 49,-0 55,-0 61,-6 61,-12 61,-12 61,-24 61,-24 61,-30 55,-36 49,-36"/>
+<text text-anchor="middle" x="34" y="-15.5" font-family="sans" font-size="10.00">all</text>
+</g>
+<!-- 1 -->
+<g id="node2" class="node"><title>1</title>
+<path fill="none" stroke="#59d856" stroke-width="2" d="M56,-108C56,-108 12,-108 12,-108 6,-108 0,-102 0,-96 0,-96 0,-84 0,-84 0,-78 6,-72 12,-72 12,-72 56,-72 56,-72 62,-72 68,-78 68,-84 68,-84 68,-96 68,-96 68,-102 62,-108 56,-108"/>
+<text text-anchor="middle" x="34" y="-87.5" font-family="sans" font-size="10.00">bioconvert</text>
+</g>
+<!-- 1&#45;&gt;0 -->
+<g id="edge1" class="edge"><title>1&#45;&gt;0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M34,-71.6966C34,-63.9827 34,-54.7125 34,-46.1124"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="37.5001,-46.1043 34,-36.1043 30.5001,-46.1044 37.5001,-46.1043"/>
+</g>
+</g>
+</svg>